ion should appear as a program called "a" in the program selection screen. Don't bother with ion, use MirageOS, CrunchyOS, or DoorsCS. All are ion compatible, and all are apps.
As for the basic files, how are you sending them to the calc? Ti Connect? TiLP? Usually, if you right click, you can choose to send to connected TI device, and I'm pretty sure you can do this with groups.