So, I've done a lot of reading up on the subject, and from what I gather it was throughout the course of the 'Sengoku' period that the samurai left their lands in the countrysides to move to castle towns where they could be more readily available to their lords, eventually receiving stipends instead of owning land. However, I what I can't find is the 'missing-link' of the transition. All I ever find is that the transfer happened, not the details of the in-between. Did the samurai live in barracks-like situations, or did they have individual homes in the cities? Families? Did they continue to manage their lands indirectly? I'm looking mainly at the Azuchi-Momoyama period. I'd love to know more about their living situations (sorry if my question is too wordy).
I'm afraid I can't give too detailed of an answer to this since this is a bit beyond the period I usually study, but my understanding of this transition was that it wasn't voluntary. Warriors didn't chose to live in castle towns, they were required to by the Tokugawa government. There were very few benefits to this. They received stipends because they were no longer able to support themselves by farming or being merchants. Samurai were samurai only, just as farmers were only farmers, and you didn't get to move around once your family decided which it was going to be. This happened in the early 17th century.
The best resources I can point you toward are the period-relevant chapters (30-32) in Japan Emerging. A few articles that I know of that might help you also include Luke Roberts, "A Transgressive Life: The Diary of a Genroku Samurai" and Marius Jansen "Tosa in the Sixteenth Century: The 100 Article Code of Chosokabe Motochika".
This transition happened because Oda Nobunaga (1534-1582) forced his samurai to live near his castle. This way he could mobilize his forces all-year-round and at a moment's notice. When his rivals realized the advantages this had, many lords also forced their samurai to live near castle towns. Thus by the Tokugawa period (1603-1868) the vast majority of samurai lived in castle towns. In this transition, the samurai were given land near the castle and told to build homes on it. Ordinary samurai got small patches of land in the castle town and built small homes that would house their families and maybe a servant or two. Samurai with greater status usually lived close to the lord (if not inside the castle), got more land and hence built a mansion. (This would make sense as they would have their many personal retainers to house.) The castle towns would normally have the castle at its center, samurai quarters nearby, commoner quarters, and an outer ring of temples and shrines.