NeoHomeBrew (./56):
Please check out the instructions HPMAN has posted there, the first thing you need to do is to change the ASM code in your "common_crt0_cart.s" and "crt0_cart.s" file and run the main loop as "void USER(void)".

Would it be a good idea to just replace old .s files with .s flies from your template insted of manual editing?