A couple of things. OS/2 uses %ETC% to put the stuff that goes in /etc in *nix systems, our TCP/IP stack for example is a BSD port. %ETC% usually points to x:\mptn\etc (x:\tcpip\etc on Warp v3).
So a good port will use %ETC%, but in the interests of saving time by porters, newer ports often use @unixroot/etc. So we have 2 etc directories.
There are a couple of ways to reconcile these.
ArcaOS ships with the klibC Path Remapper, it is found in System Setup and allows replacing/extending paths, I've never quite got the hang of it but if you look /etc is mapped to %ETC%.
There's also symlinks, these act much like *nix symlinks, at that a symlink on a HPFS partition will work on Linux and vice a versa. These only work at the libc level, so basically anything compiled with GCC (not the old EMX GCC) will see these symlinks, which are kept as an Extended Attribute. You use them with the same tools as on Linux, ln -s for example.
There's also has been file systems that support symlinks, the old ext2 port even supported hard links IIRC, as well as symlinks. Unluckily it is not compatible with LVM.
There's also the TVFS (Toronto Virtual File System) on Hobbes which also allows real symlinks and a virtual drive letter. I used to have everything linked to X:
Really, today the choices are the path remapper or symlinks, or just using the correct etc. The documentation will hopefully tell you.
Note that doing a make install on a Unix port will often install with symlinks.