You could always try doing a chapter per, alternating them. Then they could happen in 'real time' rather than telling one story and having to keep reminding your readers what the other story was up to at that point. If you get my drift. I think it probably depends on what you're planning for the end, whether they come back together or not. If that is the case, then you could have each story seperate, but update each at the same time before joining them back up. A lot more work for you, though, although fun for us.

As Bytemite says, it's your fic, but i hope perhaps my suggestions might help.

Hmm, interesting. I actually like it a bit when the crew splits up, doesn't happen often in fics, but there's a lot of potential in that for the story-telling. :)

However you feel is the best way to deal with your fic. I know when I tried to combine two separate storylines, people got really confused. You might be able to weave yours together better than I did, but it's always best to use your own judgment.