If the "application(s) that run(s) from the terminal" are X windows clients:
Assuming you haven't done magic to make one continuos display, the target screen is set via the
DISPLAY environment var (or sometimes via a
--display command line arg) with a
:0.0 for the first screen and
:0.1 for the next, etc. I.E.
xterm -display localhost:0.1
For that to work thought, you need to have X running on both of the screens, and thats beyond the research I've done for the Pi and the PiTFT (thought, it might be as simple as running two startx's, one on each frame buffer)
BTW: When I look at the adafruit FAQ on the PiTFT it talks about
fb0 being the HDMI port (and in the earlier setup
fb1 port is what is configured for the PiTFT). Are you saying that the apps currently display on the HDMI and your trying to move them to the PiTFT or are you saying you mapped the PiTFT to
fb0 (if so I could imagine there might be some problems there too)?