Best way to mine is Using RP frame machines. Takes a long time to set up, but it eats away the earth at a faster rate then a quarry. If you don't want holes in the world. build the RP machine under the surface of the earth OR make a deploy module on the RP machine to deploy dirt/cobble over the hole.
Like any way of mining in a larger scale, you NEED a way to sort the ore/dirt. Redpower, BC piping will do this for you. You just need to put in the work.