Medieval medical professionals thought they knew quite a bit about sex, especially its reproductive aspects -- what times were best to have sex, how to prevent or encourage conception, how to treat impotence or defects of the penis, how to remedy reproductive ailments exacerbated by childbearing or actively impeding it, and so on. Much of this knowledge was theoretical, being inspired by Classical medical writers like Hippocrates or philosophical conceptions of men and women's respective qualities, humoral theory, etc. Other knowledge might be closer to modern medicine in the sense of being drawn from practical experience. Widely circulated texts attributed to the semi-apocryphal woman physician Trotula addressed women's concerns like menstruation and infertility as well as women's concerns like hygiene and skincare. Theoretically, as a woman physician Trotula's access to her women patients' bodies would not have been impeded by decorum between the sexes, and she took it on as her duty as a learned physician and as a woman to lay out useful principles:
And so that from [man and woman] there might emerge fertile offspring, [God] endowed their complexions with a certain pleasing commixtion, constituting the nature of the male hot and dry. But lest the male overflow with either one of these qualities, He wished by the opposing frigidity and humidity of the woman to rein him in from too much excess, so that the stronger qualities, that is the heat and the dryness, should rule the man, who is the stronger and more worthy person, while the weaker ones, that is to say the coldness and humidity, should rule the weaker [person], that is the woman. And God did this so that by his stronger quality the male might pour out his duty in the woman just as seed is sown in its designated field, and so that the woman by her weaker quality, as if made subject to the function of the man, might receive the seed poured forth in the lap of Nature. Therefore, because women are by nature weaker than men and because they are most frequently afflicted in childbirth, diseases very often abound in them especially around the organs devoted to the work of Nature. Moreover, women, from the condition of their fragility, out of shame and embarrassment do not dare reveal their anguish over their diseases (which happen in such a private place) to a physician. Therefore, their misfortune, which ought to be pitied, and especially the influence of a certain woman stirring my heart, have impelled me to give a clear explanation regarding their diseases in caring for their health.
The corresponding humoral qualities of men and women -- women as cold and moist, men as hot and dry -- were the ideal state of equilibrium to facilitate sexual intimacy, and bringing the humoral qualities of both parties back into balance might remedy reproductive difficulties. If the woman's humoral composition is imbalanced and too hot, fumigate her reproductive organs with a steam-bath of cold herbs or apply a pessary; if the woman's imbalance is in the opposite direction and she's too cold, fumigate or medicate with warm herbs. It's hard to say if any of this actually helped in modern terms, but this understanding of male and female reproductive systems was built off of centuries of writing on humoral medicine, and it was influential across Europe.
Ideas about pleasure in sex and which positions were best and so on spilled over into the church's concern with how to do sex "right" in the eyes of God -- you might see works like the medieval sex flowchart conceptualizing the prohibitions and recommendations placed on sexuality by religious works like penitential manuals. These guides are pretty emphatically restrictive, and they do more to suggest attitudes about sex within the church and what people might have conceived of doing with each other (in a dirty-minded, condemnatory kind of way) than they do to actually describe the mundane practice of sexuality in the day to day. But from other sources it seems clear that medieval laypeople -- not just clergy writing feverish penitential manuals nor just physicians theorizing about the hot dryness of semen -- were having sex in various ways, at various times, in various places, and they felt various kinds of ways about it. Informal sexual knowledge abounded. Could you get pregnant from being raped? Could you get pregnant from coitus interruptus? Was sex with prostitutes a necessary evil, a fun pastime, or an intolerable sin? Was it better or worse to only have sex for money part-time, when money got tight, rather than full-time? Was oral sex less bad than anal sex, or more bad? Was mutual masturbation sodomy? If an adult man had sex with a young boy, was the boy blameworthy too, or just the man? Was it okay to have sex with someone as long as you were engaged with them, or should you hold out until after you were formally married? What were you supposed to do with your illegitimate children? Was it okay to have sex with somebody of a different religion? Which religion? These were questions about sex that different medieval people of various demographics at various times felt with assurance that they knew the answer to.
As for how people learned about sex in the first place -- it's not beyond imagining that medieval parents had "the talk" with their children outlining how babies get made, but by and large, medieval kids would be less insulated from the realities of sexual reproduction than modern children. Children in rural and urban areas alike would encounter animals having sex, whether that was sheep mating in the field or dogs coupling in the street, and the reproductive cycles of animals have a lot of bearing on hunting and raising livestock. Childbirth often took place in the home, and sex between humans took place pretty much everywhere -- /u/sunagainstgold has a wonderful thread on the realities of medieval sex and the bounds of privacy and goes toe-to-toe with /u/AnnalsPornographie in this thread on the relatively public nature of medieval sex and how people did it anyway. Virginity, and conception were relatively prominent topics in medieval Christianity, as were the taboos on fornication, adultery, and sodomy -- you'd certainly hear about them in church. In practical terms, a certain amount of public sexual contact might take place between betrothed and married couples in full view of others, as long as it stopped short of sexual intercourse. Knowing that your sister Dinora and her fiance Nando kiss on the mouth and grope each other right in front of everybody would have taken some of the shine off sexual intimacy in general as a sublime mystery shared only between man and wife. (But only if the randy couple are engaged. The real Dinora and her fiance were a 16th century Pisan couple -- Nando ditched Dinora at the altar and all the sexual liberties he'd taken with her in her parents' house during their engagement were cited by Dinora's priest as part of a breach-of-promise proceeding as clear public signs by which Nando effectively declared his intent to marry Dinora at the end of it all. On one occasion Nando had taken out his penis and let -- or made -- Dinora touch it, right there at the dinner table.) In urban areas with regulated prostitution, even young children knew what prostitutes did for a living -- prostitutes sometimes wore distinguishing clothing and they gathered in the open air outside brothels and apartments to chat with potential customers. So kids saw animals do it, they heard people talk about doing it, they may have encountered their own parents having sex or even total strangers, depending on where they lived they might have encountered groups of strangers calling out on the street about it. Furthermore they were vulnerable to chatter about sex from their playmates as well as sexual play, and they were targets of sexual predation from strangers. None of this adds up to a clear and unbiased understanding of human sexuality, but sexuality and reproduction were likely not a well-kept secret as far as medieval children were concerned. When parents issued recorded advice to their children, it was more often about chastity and the morals of sex -- no fornication, don't waste all your money on prostitutes -- rather than "the penis goes in the vagina until ejaculation is achieved"-style blow-by-blow accounts.
Some past threads on medieval sexuality you might like:
Mentioning previous answers is just a convenience, not intended to discourage follow-on questions, information, or debate.
"In the past when a family all lived in a 1 room house, did people just have sex while the kids played in the corner? How did that all work out and when did we start hiding sex? Did wealthy families consummate in public to prove an heir?", https://www.reddit.com/r/AskHistorians/comments/7g4t00/in_the_past_when_a_family_all_lived_in_a_1_room/ : the invaluable /u/AnnalsPornographie answers. You might read this base answer first, and then follow the link -- the link has an earlier version of most of the base answer, but adds information about theology and reform.