So I have the first foot switch set to pad ctrl, and the second foot switch set to start/stop. But it is only allowing me to use the function of the first foot switch on both of the pedals. I am using the center A & B input, and I'm not sure if that is what's causing it or if it's just a setting issue. I could use your help! Thanks

I've been using this for a few years and I feel like I made a mistake in not getting the SPD-SX instead. No Doland, it does not allow you to use your own samples unless you have Ableton live or similar software to trigger off any sounds there. Otherwise you cannot add samples to the pad like the SPD-SX can. No wonder so many people use the SPD-SX, it's just better, plain and simple

Is there a way to add your own Samples to it?

No there isn't. The SPD-SX is what you're looking for.