325iBiMMeR, I'm confused, did your car come with HK or not? If it didn't, doesn't the non-HK come with two speakers mounted in the rear deck (most call it a rear deck vs. a back dash)?
If the speakers in your rear deck are the HK subs, there's no reason to keep them, i.e., the bass wasn't enough for you, so you got the new subs. All the factory subs are doing is muffling the sound of the equipment you just spent money on.
If the speakers in the rear deck are the 6" woofer/midranges, you can also take them out, as they're not important enough to imaging to justify leaving them in and again muffling the new subs.
If you still want to cut holes in the rear deck, you have your work cut out for you. The instructions are on a BMW TIS disc, but I'll give you high-level view of how much needs to be done:
1) you have to remove the trim around where the seat belts enter the rear deck
2) you have to remove the at least the vertical portion of the rear seat
3) you have to remove the trim pieces between the rear deck and the rear window
4) after you pull out all those piece, there's some rivets on the front (behind where the seat used to be) and some screws in the trunk (think from under the deck) that need to be removed.
After all that's done, you should be able to pull the rear deck vertically, and have access to the metal plate that makes up the trunk internal "roof"
Better picture coming!