Those washers (shims) are meant to keep the various parts from rubbing against each other. So if the flywheel rubs against the crankcase, you put a shim behind the flywheel collar (collet) to space it away from the crankcase just enough so it doesn't rub. Same goes for the clutch bell and flywheel. If the CB rubs on the flywheel, add enough shims so the CB doesn't rub on the wheel. And finally, you add shims onto the very end to adjust the endplay. Add enough shims so that the CB only slides about .5mm or so along the crankshaft.
Make sense at all?