Actually, the IC2 miner pulls from Your config file, regardless if it matches the server or not. I have a custom config with numbers where all ores are a multiple of 3, diamond is 100, and lava is 1. Basically, if I find a spot over 400 it's diamonds (Or an insane amount of ore) below.
Personally, what I have setup is a track along some terrain with a powered rail every 9th spot. Storage/MFE/Anchor cart config on the rail, and in the storage is an energy unloader, 4 gold cables, two wooden chests (key), two hoppers, about 128 mining pipe (more if in a tall world), four or five stacks of cells, miner, pump, diamond drill, OV scanner, and a single redstone torch. I start on an unpowered rail.
Setup pump next to the miner, and drop a wood chest behind each so it becomes a single double chest. Drop in the drill and scanner, prime both pump and miner with cells/pipe, connect the energy unloader with gold cable to the MFE cart, and connect up the miner, and walk off. Come back, look at the hopper a minute, and if it's not moving replace all the pipe in the hopper with the cobble it mined and pull out the drill to plug the hole. Pick it all up, drop it back in the carts, and drop the redstone torch on the powered rail to move it to the next exact mark.
Lately, though, I've stopped plugging the first and seventh hole, and doing this for 7 lines and repeat the holes.. Then, I drop to the bottom of the first hole with a couple stacks of cobble, drop a landmark and a redstone torch, and hop all the way up to when the torch stops. Back at the base I have an ender-chest that keeps pulling cobble out of my exo-barrels. When I reach the end of the blue beam, drop another marker, redstone it, and hit the other holes. Then, drop the filler, set it to fill, and bam, no caves. I used this to prep an area for my overworld mob farm, but whenever I did that in the past I just felt the pang in the back that I was wasting ore.
Couple of notes though about the IC2 miner. It can sometimes leave some ore behind, so it is always a good double-check after filling the hole, but before grabbing the miner, to doublecheck with the ov-scanner and make sure you don't leave important stuff behind. This is usually maybe 1 or 2 ore blocks per miner area.