I've replaced all of my speakers and installed a sub, so maybe I can help you a bit. I don't have DSP, but I did have tweeters in my rear doors, just so you know. I have a 1997 540i.
Taking the rear seat out isn't too bad. First grab the lip of the lower seat, down where your legs would be, and just give it a good hard tug straight up. Do this on both sides, and then the bottom is free. The back requires you to first remove the headrests (just by pulling up), then remove two large bolts, one by each door at the bottom corners of the seat back. Then lift the whole thing up a bit, and pull toward the front of the car.
If you need to take the back deck out to do the speakers, you first remove the center headrest/child anchor bracket (big black metal thing right underneath the center headrest. Then you need to pull off the C-pillar trim pieces and disconnect the courtest lights that are in them. Then pry off all the clips along the forward part of the back deck; be careful not to break them. Now use a screwdriver to pry up the vents along the back window. Once you have all these pieces out, you can then lift the rear deck and get access to the speakers there.
I know all that sounds kind of complicated, but it'll be fairly obvious what I'm talking about once you get in there and see it all.
As far as bolting subs on...I'm not sure about that. The underside of the rear deck in the trunk can supposedly accomodate 2 10" subs, since that's what the DSP/M5 has. However, only some subs will fit there. Just so that I could choose whatever sub I wanted, and because I like enclosed boxes (not free-air subs, like the ones that go under the rear deck are designed to be), I just did a box in the back corner of the trunk.
So, I hope that gets you started. I didn't run wires, though, because I have no intention of replacing the head unit. Unforunately, I think replacing the head unit in the E39 makes the dashboard look crappy; in my case (540i) I would also loose my computer controls. But regardless, I'm interested to see how your install goes. Take some pics when you're done!
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