Hello Rbohlul1,
From the Bpod Console, select the settings (wrench) icon, and then the ports (Ethernet jack) icon. You can enable and disable ports from there.
Example protocols demonstrate usage of the Bpod hardware beyond LEDs: ports (Valve and poke detection), the HiFi module, the Analog Input and Output Modules, the Rotary Encoder Module and Video playback with Psychtoolbox.
If you need assistance beyond this, please share specifics about what you are trying to develop with Bpod.
Thanks,
-Josh