Homemade Corn Tortillas: How to get the back side cooked the same as the face?
Flipping twice works pretty well. Cook on the first side until that side is mostly cooked but definitely not finished (the top side should still be damp and uncooked), then flip it and cook until done on the other side, then flip one more time to finish the first side. This will likely decrease the total cooking time slightly, so expect more like 15-20 seconds on each side between flips.

If you still have trouble, you might not have the heat high enough; at a lower temperature, you're likely to cook the tortilla through and dry it out too much before you flip it, which means the other side won't rest smoothly against the pan, which definitely causes the uneven cooking you're describing. But 15-20 seconds sounds about right to me, so I'm guessing you'll be fine. (Flipping only once causes problems in the same way.)

If you really want it perfect, you could try flipping even more times, but twice has always worked pretty well for me.