Both units are individually balanced. While it's preferred to maintain the relationship between the TC and flexplate, it isn't totally necessary (I do out of habit - it takes five seconds with a small can of spray paint...)
Location of the flexplate proper is important - as the CPS reads it to generate timing signals for fuel injection and ignition. I believe you'll find that one of the screw holes is offset from the pattern just slightly - put the flexplate in place, and check all the holes for alignment. If one (or more) is off slightly, turn it to the next position and check again. If the flexplate or flywheel is going to be remounted, a small can of spray paint can help here as well (once you remove the first screw, you give the hole a quick spray. This marks the hole in the plate and in the crankshaft, allowing you to line them up easily. Once you've painted the first hole, you then remove the rest of the screws. Ditto when unscrewing the TC from the flexplate - or when removing the clutch cover. Be careful to not get any paint on machined surfaces or clutch friction material, tho...)