if i skip we will call it stage 1 and use multi level to play stage 2 and 1 at the same time. if i complete stage 2 can i move on to stage 3 while still finishing up stage 1? my exact thought is if i cant finish 2 and move to 3 i might as well not finish 2 yet and farm out all the artifacts possible but if i can move from 2 to 3 while still playing 1 i can pick the best remaining dig site and move on spend some ap and make my stage 1 and battles better.

When you beat one of the levels you are using a ML power up on, it is over, and you are back to a single level at a time.

Your strategy of staying in Stage 2 to work on Dig Sites while Stage 1 is ongoing is sound. Alternatively, you can finish Stage 2 quickly and get the AP to beat Stage 1 faster.