From talking with other keepers, from this site, and from reading relevant literature, it seems that WHERE the turtles are being kept is almost more important than HOW. I think that this is the biggest challenge when keeping all of the different species/subspecies.
I keep all of the native North American subspecies of box turtles. I live in a warm and humid climate. I have never had any real problems with Easterns, Gulf Coasts, Floridas, or Three-toes (with the exception of some fungal shell infections in the Three-toes initially). This is most certainly due to the fact that I am keeping them within their preferred climate.
Contrastingly, I have had TONS of problems with ornates until I learned some aspects essential to their care. I had to try to manipulate the environment to more closely mimic their native habitat. Deserts, on the other hand, have hardly presented any problems. I did start much later with this subspecies, though, and I had already gone through the wringer with ornates and learned a few lessons. I chalk my success with deserts up to experience with the ornates.
Obviously, captive bred animals seem much more able to adapt to different climates. You'll save yourself a lot of headaches if you start with cb animals.
I know that it can be done, but I strongly recommend against keeping different species/subspecies together.
Some general observations; Floridas like it VERY wet and humid and prefer protein over all else, Three-toes need to have the ability to dry out and will consume more vegetable matter than most, Gulf Coasts need to be kept in groups with a very high female ratio and appreciate a large and deep water feature, Easterns can be picky eaters and are more timid especially around the other subspecies, Ornates prefer live prey and seem to need morning sun and as much air movement as possible, Deserts will often not dig beneath leaves and other debris and seem to rely on burrows for shelter, Ornates will often not eat vegetation while Deserts will eat just about anything. The Eastern box turtle subspecies all seem to lay eggs in a very predictable manner...ornates and deserts nest very quickly and do so at different times.
I am sure that many have different experiences. In general, if you stick with the type(s) that occur within your climate or one similar, I think you will find that they pose few challenges.
Hope this helps. Good luck.