I agree with Rip. I've only CO'd one frame and that was a last minute deal, but I did pretty much what he said. I told squad CO's where to be, and when to be there, and what they should be flying at that time and place. This was the BoB tod, so mission parameters were pretty simple, defend the fields/targets I've assigned. Don't get suckered by Fighters. I had one complicated mission design, but I gave that to my own squadron (more because it was pretty suicidal than because it was difficult to pull off).
Esme has a pretty good thread going about CO interaction, and I must say that I enjoy when the Side CO's work together and Squad CO's offer feedback. But for the most part, I've never gotten a plan that I had a problem with. There are times when it would help if certain Squad CO's would callaborate (this one time the NHs and Shills were both in B-17s, but we never got together on an actual flight plan, so we ended up seperating before we were even feet dry over Norway). But it works pretty well, all things considered.
-Sikboy