I've done both.
I have the H/K system with upgraded under seat subs from BSW, upgraded Bimmertech amp, and added a 10" sub in the rear with custom enclosure from Musicar NW. Definitely sounds much better than stock but I'm still not too happy with it. I think the under seat subs are a waste of time and because of space limitations it's hard to put a decent sub in the trunk if you don't want to lose trunk space.
If you don't care about losing trunk space then the sky's the limit and I would go that direction!
The stock Bose system with 2 10" subs under the seat in my 14 year old Sierra Denali sounds far better than my car, sadly.
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