Hello
Brainiac!
I never used a cross compiler yet and I see no reason to do so. I'm running Geany on my PC (in order to use my standard settings), load and save the source files via ethernet from and to the BBB, and compile and test on the BBB via
ssh command line connection. For graphics testing, when your PC is running Linux, you can
use option -X (upper case) to get graphic output directed to the PC screen (as mentioned above, including keyboard / mouse input to the BBB).
Regarding your project, you can do GPIOs and generate PWM signals by using
libpruio. Once installed, it's very painless to configure (by single source) and to control (in a fast manner) the pins. It's written in FreeBASIC, but provides a C wrapper, so you can make your "master" happy.
Check out some examples: ie.
pwm_cap in order to generate a PWM puls train or
stepper in order to control a stepper motor (here single phase = unipolar).
Good luck for your project.
BR