Well I'm a newbie here too, but if it were me I'd do it to two seperate channels. This way you can play with volume/EQ/panning/effects/whatever with each mic'd sound individually. This could allow you to add depth and space to your instrument in the mix. The only benefit to recording to one channel would be that you'd be saving space on the hard disk (I think, could be wrong) So I'd say that if hard disk space isn't that precious to you, then definitely do it to two channels. If you find you're not gonna tweak each one differently, but either leave them alone or apply all the same tweaking to both, then you could always just bounce them to one track anyway. I've got hardly any equipment and I wish I could do two mics to two channels from the source at the same time. It's also a preference thing, but you'll definitely have more options using two channels.
Again, I'm new and learning as well, so if anyone reads and I'm wrong, correct me.
