Either make two bitcoin.conf files, and point the second instance at the second file using -conf=W, or specify -port=X and -rpcport=Y on the command line of the second.
Also, reconsider your thinking behind running two copies.
Running two instances is no big deal. I have six on some machines. Of course, if you don't _need_ multiple ones then you'll save space to run run multiple ones.
Give each one its own datadir and tell it about it on the commandline. In each datadir put a config file, make sure you set the port and rpcport to different values on each. They _CAN NOT_ share the same datadir. You can start off multiple copies by copying an initial one, however, but you must run with the detachdb option and shut down cleanly before copying if you do that.