They're both casters(?), which one you play as the main is probably irrelevant. The reason to play one as "the main" over another is when that character requires more attention than the other(s). If your shaman will be enhancement, you'd want to play it because he will probably require more attention than your warlock, who just stands there and casts spells.
As far as binds, any classes can be played together in pretty much the same fashion. You have a DPS rotation and then situational spells - interrupt, stun, procs, etc. All you really need to do is have your DPS rotations on one key via wow macros with /castsequence and the like, and press some other button for situationals. Some people have been combining them into one Mapped Key with 2 steps, but there are many ways of setting this up.
Here's a couple posts that have WoW macros and ISBoxer config suggestions that might be of interest to you:
Aragent's 2-step setup:
http://www.dual-boxing.com/showthread.php?t=33080Mercurio's macros (similar style to Aragent's):
http://www.dual-boxing.com/showthread.php?t=32633