I had a reply written up lsst night and when I submitted... it said i had to login. 0_o
Anyway, yes the ores are horizontal, so branch mining is the way to go.
To give an example Iron spawns about 200 ores per chunk in a typical pack. CNC spawns a max of 80 iron ores per chunk. If you go to the two ore layers, Iron is overall a bit more dense than normal so hand/branch mining is like a normal pack. Tunnel miners like a steves carts miner or tunnel bore will also be as effective.
Quarries though will net you 80 iron per chunk instead of 200 like people are used to. THe original idea was to make ic2 miners cheaper to make, and make them the cheapest way to automine, but its also the least efficient, being vertical. Ic2 miners wont pick up GT ores though 
Blockmaster used Customstuff to make custom ores, so the important GT ores are recreated using that mod, thats how we spawn some GT ores 'the old way'.
GT veins are not necessary to find to progress, they are just a bonus.
I ran out of time last night heh, my son had so much homework...
Ill get the server updated tonight and PM you the IP. 