Well, to me, recording the Main Out is resampling. You are sampling what you already sampled. And you don't need the threshold's permission to begin sampling, just hit Do It and it'll sample immediately when need to.
You will want MIDI to keep timing, but if you are resampling, then you are creating an Audio track and thats your problem of why the timing is off and not lining up.
So forget resampling, record your tracks to a single long sequence of 99 bars or more, or multiple sequences. If its multiple sequences, you will need to keep everything within the same track number, for example, Track 1 contains the snare for sequence 1. So for sequences 2,3,4 etc. the snare must be on Track 1. Track 2 may contain the Kicks, so for every sequence, the kicks must be on Track 2. That is just an example, you can have any sound onto the tracks, but use the first sequence as your template for correct playing and lining up.
Also, unless you are creating mono beats, the 500 can only track out 2 tracks at a time, so pan your tracks hard left and hard right to maintain the intended stereo image. Mute the other tracks, and record 2 tracks at a time into your DAW. If you need to record more than 2 tracks at a time, then you need an MPC1000/2500 which has 8 outs.
I hope this can get you off the ground, keep us posted.