I do ALL of the below in SONAR SPLAT:
Since I am actually a drummer first and guitar/bass second. I try to lay down guitar (rough tracks but in time with click) first. This is how I get my ideas down as far as arrangement.
After I get a rough guitar/bass arrangement, I record the drums. I do this WITHOUT the click so I can respond to any variances in timing that may or may not have snuck in. I do NOT use any kind of audio snap tools. I guess I am an old school type. The slight variances to me make it interesting as long as the timing is not a total mess.
Then if I really want it to sound good I will bring in real guitar/bass players to lay down real tracks using the drums as a timing mechanism.
Strange I know, but it works for me.