Sqwebmail & Qmail Question!

Hey guys, got a little question for the forum! This one is involving Sqwebmail. So i setup qmail, in coordination with Vpopmail, so i created a user in vpopmail, and everything is ok. I login to sqwebmail, and i can send emails, but I am a little confused about when mail comes in, where do i tell qmail to throw my inbound email, not in my /home/blah/Maildir, but into the vpop Maildir, or the opposite, i have a lot of email in my Maildir, how do i tell SQwebmail to look for my in my home directory. What should i do in this situation?

I hope this is easily understandable, if not let me know and i can elaborate. Basiclly, when people send me email to my domain on my qmail machine, it accepts the email, and puts it in my /home/bob/Maildir . When SQwebmail logs me in, vpopmail has the Maildir go to /usr/home/vpopmail/domains/blah.com/ <- and from there i wasn't able to pin down the exact file it is throwing this into, but no email is in this inbox and there is none going there, how do i re route my Maildir folks? THanks for any help!!!!