IMO I think you'd be better off upgrading to something better than Infinity especially their Basslink. IDK your specific needs (SQ, SPL, just want a sub), but its worth the extra coin to do a custom setup. I would say if you wanna do that OEM look just snag the 2004 and earlier Tibby's stock Infinity system for cheap. Heres one on eBay going for $33 with 11 hours left.
Tibby Sub
As for the aux-in I strongly recommend doing an iPod ready headunit with their iPod interface. I have had an aftermarket Kenwood unit in my car with their iPod interface for 2 years and simply love it. Once you get the hang of the specific brands navigation on their HU its great. Plus you can tuck away your iPod where ever you wanna run the cord to and it'll charge it and keep it out of sight from thieves.