How do I run two instances of bitcoind on the same linux machine with different conf files? I want to run two instances of bitcoind on my machine.

I know my bitcoin.conf file is in ./bitcoin/bitcoin.conf, and I know (thanks to this thread) that I need to change my .conf file to point to different data dirs and RPC ports, etc.

However there is only one .conf file.

How do I go about pointing my second bitcoind instance to a new bitcoin.conf file? I copied the directory with the compiled code to a new directory, I am making the assumption that compiled code can be copied into another directory and it will work without problems.
Change the -datadir flag to a new absolute location. Each instance will follow the bitcoind.conf in their respective directory.