Im installing the all balls bearings. I installed both, top and bottom bearing seals, and when i install the stem nut and the upper fork clamps it wont turn all the way! I checked and the races are fully seated, but i think that the upper seal is making the upper clamp sit too high so the notch the upper clams have touches with a "block" that has the frame... so, do i need to remove the upper bearing seal? have you had any problems not running the upper bearing seal?I've just fitted bearings from pyramid and yea it came with seals but they didn't fit correctly and I couldn't put tension on the bearings. The seals seemed to be too big and instead of sitting properly over the bearings, the edge of them would sit on the neck of the frame, which means when I put tension on the nut to seat the bearings, the nut would just compress the seals and not even touch the bearings. The bottom seal in particular would bind up into the bottom of the neck when tension was applied, making the steering feel very stiff but keeping the bearings loose. I disassembled the stem twice before realising this and cutting the bottom seal to make it fit, and removing the top one completely. This fixed the problem. I don't know the long term effects of running no seals but I can't see too much of a problem, especially since stock the bike has no top seal. To answer your question the bottom seal goes under the bearing, between the bottom triple clamp and the bearing, and the top seal goes directly over the top bearing.
Ill attach a photo to explain better...