If I read your post right (which I probably didn't, since I'm now half-dyslexic as a result of a calc test this morning...), you want to run the computer in safe mode (i.e. run just the operating system and no unneeded programs such as spyware. Running in safe mode will allow a spyware program like
Adaware to get at problems it might otherwise not be able to get at, especially if the spyware is deeply dug in. Basically (assuming you already have Adaware, if not then you would install it first), you would restart your computer, but repeatedly press F8 while the computer is first starting up. You should get a menu, with one of the options being "Safe Mode". Choose "Safe Mode," then when the computer has finished starting up, run Adaware. You can get out of safe mode by restarting the computer.
edit - you mean run it "bare-bones" while you're scanning for spyware, right? Or did I read that wrong?