All that being said, maybe it's time to come back to your original question of what works and what doesn't. Here's my humble opinion:
1. Either pick a completely closed or completely open auction. As I said, I think half and half creates all sorts of potential problems. Personally, I'd suggest a closed auction but I've proven that an open auction can be done (it's a truckload of work and you need to devote a lot of time to do it right).
2. Lay out the terms of the auction before you start. State whether it's going to be closed or open, how players are grouped (if applicable), and give a description (you don't need a concrete schedule in your first thread) of how the bidding process works. "Does one player go on the block at a time or multiple players?" " Do I bid on players one at a time or as a group?" " How long are auctions open?" "How do I submit a bid?": these are all questions you would want to at least address in your thread announcing the league. If you're running an open league, tell them it is going to take a while (ours lasted about a month or so). If you're running a closed league and you know the person who will take the bids, get that information out. That way, if someone wants to back out due to that (they have a problem with your person), it's all done beforehand and you're rid of a person who would have created a problem for you with no time wasted and no hard feelings.
3. Make it clear that everyone must agree to the terms of the auction. For instance, if you run a closed auction, make it clear to owners that by being in the league
they agree to abide by the decision of whoever has the bids. Let anyone who doesn't agree walk. Yeah, it's a pain in the butt to find owners (I'm already doing it myself for my auction league), but it's better than listening to constant whining and complaining. If anyone has an issue, you gave them fair warning about how it was going to be done.
The only other things I can think of right now are the things you'd want to do in any league you run: have a good theme, get good owners (maybe even more important here, but always necessary), stay on top of things as commish, respond to reasonable questions/issues in a reasonable amount of time, make sure the rules are fair for all and are upheld.
Hope this helps. By the way, what's the theme you are thinking of running?