Some of the bolts that are needed to attach the step rails broke off my '06. Anyone know an easy way to replace these bolts?

Extractors, get 'em from Sears or a hardware store...

The head of the bolt is still on and I cannot fit an extractor up there to remove the bolts but the head is covered by the panel below the front and rear door.

Any suggestions on how to remove that panel?

Remove all the bolts and the entire panel then drill out the majority of the bolt material with a cobalt drill bit. Then either try the extractor again , either go clock wise to screw the bolt head all the way out through the other side . Or you can go counter clockwise to extract it. I would also try the same size tap to remove the material from the threads. Yes the bolts are case hardened if you drill out enough of the bolt metal it will crumble away . It was a tough job .