In BG1 there is a point where if you beat the Iron Throne baddies all of the other earlier quests are closed out. Does BG2 have anything like this? If I go after Imoen to close out Chap. 3 can I still come back and finish the eyeless cult/umar hills/trademeet/ etc quests? Lastly for those of you that have already gone through most of the game. IN YOUR OPINION what is the "best" order to tackle the side quests to keep a good game flow???

From my experience, there is no point at which you can no longer complete quests. many people have talked about doing the critical path (ie-Imoen)first then completing the quests. A fair warning about doing that-Once you enter that process, there are a number of other things you have to do before you can get on with the original quests and it takes a while.
What you really need to decide is how important Imoen is to the party as a whole and how much experience you want before going after her.