are there special clips out there, or do you just run the front strap over the top of the clip?

That's right, front strap over the top of the clip.

Run the front strap over the top of the clip, as taras0000 suggested. You can also reverse the position of the two straps -- when they come out of the inside of the pedal, just run the back one forward over the toe clip and to the front buckle and the rear one backwards through the toe clip loop and to the rear buckle. It helps keep tackle in place better and even more important, it keeps the rear strap from digging into the top of your arch and allows the front strap to hold your foot better.