First you have to get the exact tone you want between the pre amp and the guitar amp in the room,make sure it isn't too loud.
Once you have the sound you want max out your line in level so that it is as high as possible but not clipping maybe use a pad button (if you got it) also a small amount of compression can make it a bit easier to get a sweet level but its kinda tough to use takes time if you aren't used to it can be a good thing but really bad if you don't know what you are doing.
After you get a good recording, mix all the tracks with the master at 0db then cut back the master out to allow at least 1/3 headroom for good amount to work with when mastering time comes.Make a master stereo mix and master it in some mastering software but that is an entirely different subject.