I dont get your problem with fillets, but thats probably because I too am just starting out with nurbs so I prolly don't fully understand your problem.

What I do with fillets is use the rebuild surface function to have the same number of isoparms as the edge they need to join, then stitch, check surface origins and then attach. If there is no edge exactly on the fillet edge (always really) I copy out the fillet curves and delete the fillet surface. Then I run detach on the nearest isoparm to where the fillet is (on the object to attach the fillet to), copy out its curves, delete the detached surface, then loft them with the fillet curves to create an attachable surface. Rebuild, origin check and attach as normal.

Or if the detached surface is too large, and its going to be an arse to tweak back to what it was I build patches over the two objects instead using the fillet as a guide.