Don't know if you've already upgraded stuff. I know it's been a couple months since you posted this but figured I would give my input just in case.
I have on 07 2.5i and this is what I did.
Head unit - pioneer avic-z2. i don't use an ipod but I know you can connect one to this. it is supposed to be an excellent controller for it though. Plus it has 10gigs of storage on its own hard drive so you can store stuff there as well. So far I'm upto 100 albums (don't know how many songs off the top of my head) and have only used about 30% of the storage space. Plus it has navigation which I love. I paid roughly 800 for it. Here's a picture:
As for the sub I built a fiberglass box in the spare tire for a single 12. I did this so I wouldn't have to move it when I needed to use the hatch for storage space and with the spare tire still there if I get a flat no problem at all you can just pull the box out then the tire. Here are some pics:
It has the stock floor and sounds amazing even with the floor covering it.
Hope this helps a little.