I've used 4x5 tanks with SS hangers, drums, deep tanks with film clips, and just about every combination in between. I've used hand agitation, rotating drums, and nitrogen burst. I have even done it in a tray but not E6 and not at 100 deg F. That is one thing I would not try to do.
As long as you adhere to the time, temperature and agitation recommendations of the manufacturer for the method you choose, you probably won't go wrong.
I must point out a few things. Best results are usually obtained with either Kodak, Fuji or Agfa chemistry. All others appear to have some deficiency or other AFAIK. Another is that E6 processes with a blix instead of a bleach then fix tend to allow more silver retention causing problems in highlights.