I play the song and imagine the drums playing in my head and then find the rhythm in my drum software that sounds like it. Sometimes I have to rearrange the kick and or snare to get what I want. Even when I get a good bass performance I find I need some minor moving of notes to align with the drums, really makes a song sound so much tighter when you do that and I find it kind of fun to do. Read up on audio transients in cakewalk editing.
I like MEquilizer to dial in my rhythm guitar sounds, it's a free plugin. You can boost or cut a tone and then sweep it back and forth to find where it sounds good. If you haven't watched any creativesauce youtube cakewalk videos yet I found him really helpful to learn how to do things in cakewalk, he puts things in a simple understandable way.