I'd like to listen but my spyware filter here at work is blocking the download page.
"The link you are accessing has been blocked by the Barracuda Web Filter because it contains spyware. The name of the spyware is: Spyware.Exploit.Misc.MDL.dl.box.net"
There are a ton of answers to that question.
One quick tip, make the kick drum hit at the same time as the bass note. That will give you some thump to go along with the boom.
Pro tools is the LAST program I'd recommend for someone just getting started.
You are limited in what hardware you can use. I hate that.
I'd go with reaper. It's free to try and only around $50 to register. You can use any interface you want (I've heard that the mbox series kinda sucks) A line...
Could be a setup issue, if you bass isn't properly set up for pop n slap you could be getting clicks from the strings hitting the frets or pickups. If I'm not mistaken you want a little bit higher action for slap bass.
The main thing I noticed after treating my room is that sound becomes more directional. The guitar sounds like it's coming out of the amp not from everywhere in the room.
Frank beat me to it. One room would be way better.
Edit: Oops. Posted at the same time as you did.
If you are dead set on doing two rooms I'm not sure how you could do much better than your plan there.
You are going to have some difficulty achieving isolation when you are in such close...