YOu battery is under your rear seat. There are two latches and the seat comes up easily.

Factory amp is behind the drivers side wheel well. Cheap unit that might put out 15-25 wpc.

I just went through this exercise with my 98 E320.

Changed all the door speakers:
New Focal 7" components fit in factory locations with tweeters in the a-pillars - excellent crisp sound powered by conservative 75 wpc. If you take off the doors and need a kit to fit the speakers, I know where to get one (German company)

Rear door locations have focal 4" coax powered by the Nakamichi head unit. Only for rear fill.

Opened the four 7" holes in the rear deck to port a single 12 inch Image Dynamics sub built in a custom enclosure that fits behind the drivers side rear wheel well - NO loss of trunk room. 300 watts for excellent low bass response. As someone pointed out, the trunk is very sound proof with the gas tank betwen the trunk and back seat. It actually makes the car more quiet. If you want your bass to be hard hitting, you will need a second 12" woofer behind the other wheel well. There is also the possiblity of using the spare tire well to add subs. In fact, if you really want to get creative, you can leave in the spare tire and build a sub enclosure that will drop right into the middle that will hold a 12" sub, so you could have three if you wanted.

You can see my install at:
http://www.sounddomain.com/member_pages/view_page.pl?SID=GAT80WMMLE4rRQsyQg__&page_id=133487&make_type_query=make=Mercedes-Benz&model_brand_query=model=all_models&tree=Mercedes-Benz%20(all%20models).

I walk through the construction of the custom enclosure. Send me an email if you have questions.

Good luck.