Your idea is exactly right. Use plywood or similar material to distribute your weight while you're on the roof, and use soft material--carpet (with the backing side up), blankets, padding, what have you--underneath the plywood so as to prevent damage to the EPDM membrane as you move about. We used particle board and an old blanket while working on the roof of our 2363, and had no issues whatsoever.
Matthew and Lisa
TT: '02 T-2363;
TV: 2012 Ford F-150, 4x4/Off-road, 5.0L V8, "Big Gray"
Reese Straitline w/ dual cam