If you are in a small room and layering, you are going to have to go with close mic'ing. The lack of clarity you are experiencing is because the sound of the room is building up on your tracks. Mic'ing an amp from 4 feet away (unless it is cranked up really loud) requires a really dead room. Otherwise, the midrange will get smeared by the 'ambiance' of the room. It isn't a big deal with one or two tracks, but once you get 10 or 12 tracks with the same room sound, you've got problems that eq won't fix.
You should also try to do your vocals in a different room than the guitars. That will help because the other room will have a different sound to it. You could also get closer to the mic.