I went through this about a year ago. There are TONS of megasquirt info on the internet. This specific forum especially.
But to try an answer your questions...the expansion card will take over some features that the standard board would usually do and add features that the standard board can't do.
You do not HAVE to purchase a variable TPS, though it is highly recommended and will help out a lot in tuning and using the features that depend on the throttle position. I wired up a Wells 201 TPS with mine and makes things much easier.
I am still in a confused state with how the IAC works with the MS. Personally, mine wouldn't idle low enough with it, but with it capped, it idles fine except for when the car is cold. It has to do with idle settings in Tuner Studio that I have yet to figure out, but there is info all over.
I don't have air conditioning but there is an idle up feature in Tuner Studio, so there is probably a circuit for that, but I never payed attention to it. I'm sure someone can help you out with this.
Hope I helped in some way, but I'm still a noob myself. It's an experience indeed. Feel free to check out my MS3X build thread. I ask a lot of questions so it may help clear up some things for you.
Oochi's MS3X DIY Build