Aux will not work on radio

[BigSteiner5]

06 f350 stock 6 disk radio. my battery died yesterday and now my radio and cd/player work when i turn the truck on and will continue to work until i hit the aux button which my itouch is connected to. when i try to change back to fm/am nothing shows up but the little headphone thing and when i hit cd player it keeps saying initializing 3 and stays like that... i have to turn off the truck and restart it to get the radif,/am/cd to work again but now my sirius and itouch dont work. any help would be great thats guys

[Motown Fire]

How do you have your mp3 player hooked up to your aux ???

[BigSteiner5]

i guess it just an aux wire. you plug it into your itouch headphone thing then the guy ran it to the back of the stock headunit. it has worked for the p.o. and it has worked for me for the last month until i jumped the truck the other day because the battery was dead. is there some security feature? but then my am/fm wouldnt work either but it does until you hit the aux then you cant switched back to anything unless you turn off/restart the truck