I started by adding an amp and a some subs(still using the factory HU). I had a problem getting bass in the cabin so I punched out the ski hole(like you plan on doing) and it did help but I still want more. So now I am going to remove the rear speakers and mount 2 10's in a free air (when the speaker uses the trunk as the box) set up. Once the subs are taken care of I am going to add a 2nd and 3rd amp to power the front and rear mids and tweets.
Although it takes awhile doing it in stages helps you appreciate you upgrades and you can save money for better performing products.
18 inch Alba Bertha's
BMW accessories 2dr. front bumper
/////Alpine PXA H600
(3) JL Audio 8w6's