I actually have not had any issues handling the 3 UY's we currently have. I use each membership separately and on very rare occasions have transferred points from one into another. I have reminders of each banking deadline set on my Google calendar.
One of our UY's (poly/BWV) has 3 contracts at two different home resorts but even in that UY I usually use the contacts only at their home resorts. The other two UY's are single contract/home resort memberships. One I use the points only at that home resort (BLT) and the other I use more often as sleep around points (BRV). The contract in ROFR currently will be used for the trips that we tend to book only a few months in advance since we've moved to Florida.
I think I personally would have a harder time keeping things straight if I had contracts at the same resort in different UY's. I know my limits!