I would say that if you have a direct out, you might as well record that too. You never know, a little bit of it mixed in with the other two mics might sound awesome.
I would also try experimenting with slight panning of those recorded tracks when you get them down. Try the 57 full left, with the 990 pulled to the center a little bit (or vise versa). Done with two guitars, this really seems to thicken the mix. In my experience at least. Something to try at least.
Currently I record through a Randall ISO cabinet with only one mic... so I have to resort to recording at least two tracks per guitar for each song. Lots of record, mess up, repeat until I get two cleanly played and well phrased takes.
Also, when mixing, I would reccomend listening to each recorded track solo first to find your starting point. Listen to the 57, then listen to the 990 to see which one sounds better on its own. Maybe (not likely) the line input is best?
I would rank them 1-3, then start with #1 full volume. Then start to turn up #2 until it sounds the way you want. Then start to turn up #3 to see if that sound is even necessary. The best sound might be, for example, 80% volume of #1, 50% volume of #2, and 15% volume of #3... not 100% 100% 100%... or 60% 60% 60%, etc.
Just thought I'd throw that in. Have fun!