Before I begin the Auto Setup should I tell it my speakers Sizes and crossover? I'm running Amrita Jovian Pillars (plus center speaker from Amrita, bookshelf surrounds and a powered sub) that go down to about 45 which I consider having good bass down to that point but I believe I read somewhere that you should set all your speakers to small even though you might consider them large. So before I begin the Auto Setup should I set them all to small? And to what crossover?

I couldn't wait so I went ahead and tried the Auto Setup but I did set all my speakers to small and the crossovers to 80. It went fine but after the Auto Setup it changed my speaker sizes to:
Front=Large
Center=Small
Surrounds=Large

Why did it change my settings, I guess I don't care if my Fronts are set to Large but not my Surrounds? Since it changed them do I just reset them myself and everything will work fine? I did change my XOver on my Fronts to 60. Also before running Auto Setup should my Sub Xover be set to minimum and what about it's volume?

If I end up running all my speakers to Small can I still run my Pillars full range when listening to cd's? Could I also in addition to running Pillars full range run my sub (for a little foundation)