It can be a simple as editing main.cpp loop function in the mystorm dir:
// You code here
uint8_t send = 1;
send = 0;
cdc_puts("Hello from my BIMx code\n");
// End your code
mode = !Bui.mode_toggle();
There is also a setup function called first which you can also add code too.
Then edit the make file and point to where your ARM tools are, then you can
make dfu to upload
(Make sure you hold the Boot/mode button down when you power it for DFU mode)
(Also use the latest firmware version USB-CDC-Issue-3 branch)
The advantage of doing it this way is you can still program the Ice40 and Flash, just remember not to hog processor time in order to allow it to still do the Ice40 stuff.