I think the subject says it all. I finally got the games running, but they are impossible for me to play if I can't invert the Y axis.

I can't see any evidence of the option in the original Incoming... but it's definitely in Incoming Forces. Look under Options, then the Controller configuration - it should apply to both mouse or joystick controls.
Out of interest, what OS do you have, and how did you get the mouse to behave acceptably in the original Incoming?

Oh I didn't really try incoming only forces. I think when I tried incoming the ship started spinning like crazy. When I said I finally got it working, I should really say finally got them running as I had some issues with both games not starting. My OS is Win7 x64 and it was funny cause both games would give me some error about not being able to find a file, and I had to uninstall and reinstall with a directory name of incoming not "incoming and incoming forces" which was default for the installer. I think the games didn't like the spaces or the path to get to the directory was too long.
As far as the invert Y I don't remember seeing it in the forces options. But I was running through the tutorial so maybe it is only at the main menu options. I'll have to look.