Wanted to share my thoughts and learnings as I've been reading up on this in old forum posts over the last few weeks as i'd like a bit of extra bass too. I have the same system as you, except i've replaced the head unit but still not happy with the sound.
I think you will struggle to power any form of sub in the boot or cubby holes without an amp.
I think the max size sub woofers that will fit in the cubby hole space would be 6.5" on some kind of MDF mount. However this size is relatively rare, most are 8, 10 or 12 inches. And from reading other posts people who have mounted 6.5" subs in these locations say the result wasn't quite as good as they expected, and in heindsight they would have mounted 8 or 10 inch subs in the boot.
Although subs in the boot come with their own problems such as rattles so some sound deadening may be required.
There's the option of removing the rear parcel shelf to reduce rattles(plastic bit in the boot), but someone pointed out that when this is out and the roof is up people could see directly into the boot.
I'm still a bit unsure on what to do, I think I am going to put one or two 8 inch subs in the boot, possibly in a custom mdf box unless I can find a premade box which is under 30cm in height and depth. I will then install a basic amp and run this off the aftermarket head unit.
I think you can still run an aftermarket amp from the business head unit, but you may need an adapter (not really looked into it so could be totally wrong here).
My guestimates are, amp £70, Subs and box £100-£150. Nothing fancy, just some cheap Fli's or something to provide some bass.
Was also looking at upgrading the front speakers, 6.5" in the footwells (but you need to make some mdf adapters to fit oem holes) 4" (10cm) in the door. There's currently no speaker in the door. Other people have tapped into the feed to the tweeter which is apparantly full range, and run a mid or 2 way 10cm to the door.
What my plan is for the front to start with is, keep the existing footwell and tweeter. Buy some secondhand OEM BMW 3 hole mids for the door (for quick and easy fitment) and run off the tweeter feed, and fit the subs.
If this doesn't provide the sound I want, I will then look at replacing and possibly amplifying the fronts, but that's when it starts getting expensive, time consuming and space wasting.
Hope this helps.
Dan