I owned a shop for a while that sold JL Audio, and in terms of sound quality, fitment, build quality, etc. the stealthbox line is one of the very best. JL spends a lot of time getting the sound quality as well as the fitment spot on. You will pay for it, though, and the others observations are valid, the one for the M3 is huge, and is placed in a bad spot.
Pros: Sound Quality, Build Quality, Fitment.
Cons: Price, Size, Placement, Weight.
In terms of the correct amp and installation method it really depends on what you expect. There are several options and methods that will result in differing levels of quality, quantity, and adjustability. You can not go wrong with a JL Amp, they are the real deal. You are going to have to rely on a seasoned installer to direct you to the correct setup for you. Make sure you spend enough time describing your expectations so they can get you in the right product mix.
PS, I had the E36 Stealthbox as well, and it was fabulous. Not particularly loud, but very smooth and accurate. It was really a completely different animal than the current E92 setup.