Awbimmer: I think you should change the jumper pin on the xover to one pin less than it is now. Quite a few people do this so not to worry its normal due to them being on axis.
I can give you a quick base to test, although i never had a sub in my car. I'd set the Jehnerts at 80hz HP @ 12/24db and 200hz LP @ 24db. Morels HP 200hz @ 24dB. For your sub you can experiment on the LP (up to 80hz i'd say) but you might want to set the subsonic to 20-30 depending on the sub and power going to it.
The key to getting a good calibration is to make sure that when the ms-8 does its sweeps in each channel during calibration, that all channels have the nearest dB level you can. So really you should focus on doing this. Obviously xover points and calib volume will come into play but if you have it all level matched first then you don't have to worry.
But as you have a sub it's going to take a bit more trickery to get it sounding good. It can, and has been, done before. I'd guess that you will benefit from doing one of kaigoss' mods; makkan knows about this.
2008 E92 335D SE
2010 E90 320D SE
1994 E36 318I SE
1996 E36 316I SE