From @gbolo on Wed Aug 17 2016 02:41:45 GMT+0000 (UTC)
ipfs expects it’s config file in $HOME/.ipfs/config, unless IPFS_PATH is set, then it looks at $IPFS_PATH/config
For multiple deamons just set a different IPFS_PATH for each and make sure that their listener addresses (and ports) defined in the config do not overlap .
Copied from original issue: https://github.com/ipfs/faq/issues/162