Flash apps are always stored in ARC, even when run. Programs (including BASIC ones) can be stored in ARC, but they have to be put in RAM when you wan to run them. Also, apps cannot be edited, whereas BASIC programs can be.
As to your linking problem... I have no idea. Since TI-Connect correctly recognizes it as a 84+SE, my only guess is that your calc may have powered down when you were trying to send it your BASIC programs. To be sure, next time you try sending the programs, check that there is a blinking cursor on the calc's screen. If there isn't one, press the On button to turn the calc on. Sometimes it won't work when plugged in to USB, so if it does't turn on, unplug it, turn it on, and then reconnect it.
