It's a huge problem to tackle. I've tried thinking of all sorts of ways, but none of them are entirely satisfactory. I'd suggest going the Dwarf Fortress route and just depicting it top down on one level and show the outside as normal and then the inside surrounded by black (or some other fill colour to depict solid rock). And pretend there are no other levels. If you find levels to really be necessary, map them separately as a match for the ones above or below it, again like Dwarf Fortress does.

I looked up mining maps to see if they would be useful, but talk about complex maps. The old ones are usually elevation type maps showing the different levels of the tunnels, which whilst cool, is not really useful for gaming purposes. In modern operations they do these wild 3d maps with all the different rock types and ores they found on the way and estimated findings furthur in the rock. The modern stuff is extraordinarily expensive to get software for, and really entirely useless for our purposes here.