It starts wow in the order you have them in the profile editor. If you look at the Character Name windows while the system is active you will see which WoW window GCP thinks is which by mousing over a WoW window and whichever turns green.

You can manually point GCP at a window by clicking Layout/Disconnect from Windows then click on each character name window in turn and mouse over the wow window for that character and click space.

I hope this explains what you were asking for.

Yes it does, I'm having trouble keeping track of what window is which char/account during setup. I think I may have one of my layout where the logins are different than what GCP thinks they are. Any way to manually edit them? I remember reading about a file where they are stored somewhere on the site.

When you do your window editor maybe it will be less of an issue (just drag joe the druid over there).
-Greg

Just load that layout and login. Then click Layouts/Disconnect from windows. Then click a character window mouse over its window and hit space. Do this for each character then save the layout again.