I'm just starting to use TolAnalyst, and I've run into some of these same problems. The documentation for this add-on is exceptionally bad, but this is what I've determined so far:
Float fasteners is not restricted to toolbox parts. My current understanding is that any concentric cylinder and hole with radial clearance can be subjected to the "float fasterners" option.
Regarding the bearings: Are you trying to add the bearings as constraints on the shaft? In other words, is the shaft the part currently active in the parts list, and you are trying to add two concentricity constraints to it? I have found that you cannot add two coaxial concentricity constraints to the same part. Try changing the assembly order from bearing-->bearing-->shaft to bearing-->shaft-->bearing, then add one concentricity to the shaft and the other to the second bearing.