You're of course right that the core of location for a new house or dependency (which could actually have as few as two monks) was a negotiation between the secular patron and the religious founder. And it was often a negotiation indeed: prospective Cistercian communities and nobles had similar ideas of what land was already valuable, in many cases. The standard hagiographic "vision that seals the house's foundation as miraculous," in some cases especially in France, was sometimes also wielded as confirmation to the skeptical noble that a house needed to be in that specific place.

Within this general framework, there are a few things to consider. The first is the most generic "where," region/country. With the Cistercians, scholars have pointed to a couple of patterns. First, the need for "Christian pioneers" in an area with few monasteries at the time. Large swathes of England, apparently, but also regions teetering on the edge of Christendom in more ways than one. Cistercians from Europe insisted, over and over, on a Cistercian presence in the Levant despite the apparent difficulty of sustaining communities: many of the late 12th and 13th century foundations there were actually re-foundations of abandoned communities. Cistercian monk Peter of Ivrea even became Latin patriarch of Antioch in 1209. In the regions under the scope of the northern/Baltic Crusade, Cistercians were not only active in mission work and economic life, but individual abbots sometimes became some of the wealthiest and most powerful local lords because of it. And during the Latin world's brief foray into attempting to rule Byzantium, Western bishops and abbots sent Cistercians to establish a Latin presence in Greece (actual Greece, yes).

Second, within the broad regions, and often affected by general and more specific location, there were a few options for establishing a new Cistercian community. The first was to "reform" an existing house, that is, to introduce new leadership from outside, new liturgies, a new Rule if applicable, usually new austerity and zealousness. The second was to move into an existing but abandoned property. This was common not only in former Cistercian houses in the Levant, but actually also in Byzantine territory--Cistercians moved into or built next to abandoned Orthodox monasteries and churches.

The third factor is the most "Cistercian" and also the most historiographically contentious. The general narrative of Cistercian expansion in western Europe fits in with the pioneer idea. They took over empty land that no one wanted and turned it into productive farmland. In particular, they're known for draining a lot of Low Countries marshland. This fit the two Cistercian ideals of "flight from the world" (living far from other habitation) and manual labor (disciplining the body through work). Although the Cistercians were indeed quite important in increasing agricultural production, this part of the story is a little overblown. Especially the smaller dependencies might be pitched closer to towns for pastoral work, at least in the 12th century. But the most significant impact of the Cistercians over land practices/determinant of their location was consolidation. As peasants and even some aristocrats oriented their lives more around towns, villages closer to towns, centers of market activity, there was a lot of land beyond that was held by a patchwork of owners somewhat akin to the crazy gerrymandering maps of current U.S. electoral politics. Only rarely did they take over truly never-developed land.

The Cistercians were eager purchasers of these plots, and patrons seemed to be generally pleased with this arrangement. Function in both economic and religious terms was a key decision in the foundation of communities, especially visible through which order(s) a noble supported. For example, as attention and visibility shifted to the mendicant orders in the 13th centuries, nobles like Jeanne and Marguerite, countesses of Hainaut, shifted patterns of patronage from Cistercian houses to Franciscan and Dominican men. But importantly, they did not equally patronize Franciscan and Dominican women, who after all, lived the lives of cloistered nuns. Instead, they supported beguine communities--that is, women who lived active religious lives in the world, through teaching or textile work or running hospitals.

It's important to recognize that original location was often strategic in the long term sense, not just immediate. Especially with women's communities, growth and flourishing was often the result of decades of shrewd management, awareness of local economy, and slow, calculated purchase of land as well as received donations. There are some cases in the 13th century where a Cistercian house received one of their famous granges all in one piece, but this was far less common than consolidation of existing less than huge tracts of land.

Finally, there is the most intimate level: so you want to found a monastery. Some nobles intended to enter their own new community, and would reach out to the local bishop or perhaps a community with which she or he had ties already (including family ones). Older, more famous, and wealthier communities served as a sort of central hub for connecting patrons and religious founders--it's often the case that a noble contacts a famous existing house, but the actual delegation headed for the new foundation is from a second house that the first had already established. Bishops might play a similar role in connecting patrons and founders--or they might simply be the founder. For example, the Bishop of Wurzburg founded a women's community at Wechterswinkel in 1144, and then the nuns (with his support) had to persuade the nearby men's community at Ebrach to supply necessary pastoral duties.

Giles Constable, The Reformation of the Twelfth Century, is still really good for stressing the spiritual aspects of the reform. Constance Berman's work on the early Cistercians will get you into the nitty gritty analyzing charters and hagiographies to figure out exactly what was going on. One of my cohort is writing her thesis on monastic foundations in Central Europe and, who knows, might completely overturn all of this. And finally, although I usually hesitate to recommend these, the Cambridge Companion to the Cistercian Order is one of the most readable out there for someone with a basic medieval background, for which you waaaaay more than qualify.