#1
What is the best program to use to get atmospeheric backing tracks like in Vai, Satch kind of music.

I'm guessing synths are mainly used but I dont have the first clue about any good ones. I know how to use them to get sounds you want but I dont know of any good ones that are versatile enough to get many different sounds.
#2
The Line 6 Spider III's have some effects like Chorus Flange, Tape Echo, Sweep Echo...
Combine those two and you get some really space/atmospheric like sounds.
Throw some Reverb in there too.
Jackson King V KVX10
Line 6 Spider III 75 W.
Peavey 5150/6505 Combo to be owned at the end of 2010.
#3
^ Yeah, great idea, synths through a mediocre guitar amp.

Generally you'll be looking at MIDI synths and drums for home recording, they sound a little thin and digital, I doubt that it's what the pros use though.

Check out Tweak's guide (google it), there's a whole section on MIDI.