Travis - I had the Scosche deck mounted in my trunk and it runs off an app on your phone. Worked ok but had some issues so I went with the JL audio bluetooth hookup that plugs into my amp. I am only playing off my itunes playlist anyway so I control everything on my iphone. Super clean and easy plus only $40.
http://www.jlaudio.com/mbt-rx-marine...receiver-91126
I also saw this at SEMA this year.
http://mbquart.com/polaris-audio/blu...-audio-remote/ Its small but gives you the control in hand vs on your phone.
Bluetooth is the direction everyone is going so just search and you will find all kinds of options if you aren't married to CD's and FM.
Best of luck