Hi Tanner,
If you want to modulate the intensity of a "Chip on board" LED, you can use the analog output module to drive Sparkfun's FemtoBuck LED Driver (or PicoBuck if you need more channels), or BuckPuck if you need more power.
The state machine onboard hardware does not have the ability to store a waveform and play it back, unless you need a simple repeating pulse (e.g. this example, using global timers to flash LEDs in parallel with the flow of states). For light intensity modulation beyond "on" and "off", you'd need the analog module.
-Josh