Signing posts is fail. just saying.
Those ores are linked to different mods for example Forestry i believe adds a copper ore, IC2 adds one and im going to go ahead and say build craft? You can disable that from happening but youll prob have to redo your world for new generation.
Sorting that will be a pain, although im pretty sure all the mods can use each others copper I think? Anyways on to you furnace problem, Items go in the top to be smelted, power on the bottom and then Extracted from the back. If you have several furnaces lined up in the a line, you can use iron piping and steer where you want all the bars to head down, or use a combination of cobblestone piping and stone piping as they will not connect to each other and give separate pipes