I have covered these questions for the passengers and crew of a retourschip – a Dutch East Indiaman designed to make the return trip to Indonesia – in 1628 (the longest single voyage then commonly undertaken anywhere in the world), so you might like to take a look at the relevant excerpts from my book on the subject. I'd add that the most senior passengers in the stern would have had private cabins, chamber pots, and a designated servant to empty them, but this applied only to a very small number of the total of the passengers and crew. For everyone else, life was as depicted below – and remember, what I'm describing here is very much the top end, the state-of-the-art, for early 17th-century seafaring:

The shock of life at sea would have been considerable… Within a week of sailing even basic cleanliness became a dreamed-of luxury for the passengers and crew of a retourschip. There was no fresh water to spare for washing, and although one of the largest ships of her day, with a complement of nearly 350 people, the Batavia was equipped with no more than four latrines. One pair was located on either side of the Great Cabin, and reserved for the use of the people in the stern. The rest of the crew had to queue to use the remaining pair in the bow, which were nothing more than holes in the deck under the bowsprit. These heads were open to the elements and the gaze of all those waiting in line, and the urine and excrement deposited in them dropped straight into the water. The only additional amenity was a long, dung-smeared rope that snaked through the hole in the latrine. The frayed end of the rope dangled in the sea, and could be hauled up and used to wipe oneself clean.

This miserable existence was compounded in bad weather. All the gunports and the hatches had to be closed and battened down, and little fresh air penetrated below deck. The men stank of stale sweat and garlic (a popular cure-all at the time); everything was permanently damp, and it became too dangerous to venture to the latrines. Soldiers and sailors relieved themselves in corners or crouched over the ladders down to the hold – when the stern of the Batavia was salvaged in the 1970s, archaeologists discovered large quantities of a black, phosphate-rich substance inside the hull; analysis revealed the presence of gristle and cereal husks, suggesting the black mass was a layer of human faeces deposited in what had probably been the bilges – and if the weather was bad enough for the pumps to be called into action, the urine and faeces that had been deposited below made an unwelcome reappearance. Rather than discharging into the sea, the Batavia’s pumps simply brought up filth and water from the bilges, ‘fuming like hell and reeking like the devil’ as one contemporary put it, and sent it cascading down the gun deck to slosh around sleeping seamen until it found its own way out through open ports and sluices. When the weather finally improved, the men would scrub the decks with vinegar and burn frankincense and charcoal down below in an attempt to clear the air, but for much of the passage the lower decks of the Batavia smelled like a cess pit in a tannery. Those fortunate enough to travel in the stern were spared the worst of this, but every account of the journey east makes it plain that, during the first weeks at sea, even the most distinguished passengers endured discomforts they could scarcely have dreamed of back at home.

...When the winds dropped there was relatively little for even the sailors to do, and for the soldiers, merchants and passengers on board, day followed day with scarcely a break in the general routine.

In these circumstances, food quickly became a subject of consuming importance for the inhabitants of the Batavia. The passage of time was marked by the hot meals that were served three times a day: at eight in the morning, noon and 6pm. These could be grand occasions; Pelsaert and Jacobsz. ate in the Great Cabin, usually with the ship’s senior officers and the most distinguished passengers as guests. Jeronimus Cornelisz. and Lucretia Jans. must have dined at the upper-merchant’s table, along with Gijsbert Bastiaensz. and his wife. Claas Gerritsz. the upper steersman would have been there too, along with his deputies, the watch-keepers Jacob Jansz. Hollert and Gillis Fransz. – whose nickname, somewhat unnervingly, was ‘Half-Awake’. Further down the table sat the provost, Pieter Jansz., who was responsible for discipline on board, and perhaps some of the junior merchants: young VOC assistants such as Pelsaert’s favourite clerk, Salomon Deschamps of Amsterdam, who had been with him in India. But even these privileged people could not take an invitation to the merchant’s table entirely for granted, and there was another well-stocked table in the passenger accommodation at the stern to which they might occasionally be relegated and where the likes of the predikant’s children and the less favoured merchants and officers ate. Here and in the Great Cabin there were napkins and tablecloths, pewter plates and tin spoons, cabin boys to bring the food and the steward to serve wine. The sailors and soldiers, on the other hand, dined where they slept, sitting on their sea chests and eating from wooden dishes with wooden spoons. There were no servants before the mast. Instead the men were grouped into messes of seven or eight, and one man from each mess acted as orderly to his shipmates in weekly rotation, fetching food from the galley in pails and washing the dishes (in salt water) afterwards. The cook and his mates ate last of all, standing watch while the rest of the crew had their meals.