The order of a CD is automatically maintained with an audio CD, but with MP3 CDs, it depends on the MP3 CD Burning settings you select. Your MP3 CD player has an inclination to play the MP3 files in alphanumeric order. Click on the MP3 CD Wizard that appears to the right of the song list when you are in MP3 CD mode. If you choose Standard mode, the song order will be preserved. In Fast mode, the song order will not be preserved. Finally, you can Specify your settings and choose to preserve the song order.
In regard to the earlier problem, I'll file a problem report. I can't think of a workaround right now. How many song lists do you need to merge with special mixing settings?