As long as you have User Defined Parameters Will will make the "base" tables for you. If you want different axis in them such as the lt4's vs a trucks then you need to specify that up front as you won't be able to change the axis after the fact. Will will also set the maximum settings to adjust the tables too. You will then edit the tables using the xdf file Will sends you. If Will edited the tables - went ahead and put lt4 tables in for example (I recommend this) then all you have to do is open an older file you have with the xdf file to see what was in it previously.
I did not know there was a second iat2 switch input, so you found something else there.
Since you're working on a car the rate table isn't 100% necessary, but it is nice to have it as it is different even between the cars vs the lt4's. I'll attach some pics at the base of this illustrating how to adjust them. Still have to do a lot of screen shots for the big write up... Will also has a pretty involved day job on top of all of this now. Another reason I'm not jumping to post everything
Main tables you need - sciap offset and linear / manifold volume if your OS doesn't have it / throttle rate / pedal progression / sciap factor / supercharger equipped you should have / the iat2 you found?
Other tables you might want to get - accel based limiters - there's two of these / tcs settings (these were thanks to Verlon)
After all of this you'll need the sciap wired in like a lt4's and the lt4 map wired in like a lt4's since you have a car you can take the temperature input straight to the ecm - you can verify with Will as I know Will has done this. You should go to using the iat2 for your timing changes (maybe this is where that second switch comes into play now that I'm thinking about - haven't fully confirmed the timing controller part) and basically have a mostly factory lt4 controller after all of this.
Edit - Will already responded Also looks like Will has already messed with that switch some.