The first thing on the interface is which way you want it to dig. (IE East South maybe even North-west?) Next you choose how long the tunnel they dig is. EX 20 blocks 60, 90? Then you choose a pixelmon(s) out of your PC. and it would have to be a Rock or Ground type pixelmon.
Then the pixelmon start digging. But some pixelmon would dig faster then others IE Groudon would be the best and roggenrola would be the slowest. The pixelmon would then walk to the stone dig it out then carry it back to the Digging block or whatever it is called and store it. then you could leave and come back later and grab the ores and stone they have mined.
And maybe some pokemon have special abilities for example if you have a Dugtrio digging he would act like fortune and maybe get you extra diamonds or coal if they found it and if you have camerupt digging any iron or gold they find would be smelted into ingots.
Anyway that is my idea i hope you liked it or at least got some inspiration from it.