they've got a 3-prong jack that goes into the mic. but the other end which is going into the multitrack recorder can either do a 1/4" or the 3-prong dealy. is there a sound quality difference?
would i get a better tone quality if i ran the mic and the direct out into the multitrack?
and where do you place the mic (sm-57) in front of the speaker?
I tend to record straight from the line out into the computer mono input
you only get mono but it is a perfect replica of whats going through the amp and does a farily good job of vocal aswell
Different placements give different sounds - experiment!

The 3-prong connector you speak of is an XLR, use these cables where possible as they are balanced and this helps prevent interferance.