I set things up so that the ROMs stay in the standard RetroPie location, but all of the RetroFE collection assets (artwork, videos, metadata) remain separate from the rest of RetroPie in their own collection directories. So if you want to use RetroPie artwork assets, you would need to change the collection settings.conf file to point to the right EmulationStation media directories. That choice was intentional - the ES scraped artwork assets tend to be garbage. With this setup, you can download the preconfigured RetroFE collection assets from EmuMovies, copy them into the RetroFE collection folders, and just rename the collections to match the RetroPie system naming standard. You may need to make some tweaks to the collection settings files though, to point to the right system metadata. You can refer back to the 'genesis' collection that is created during the install process for a configuration example.
Here are the places to look at for setting things up...
If you enable the Samba shares via retropie-setup, then you can use the following shares over the network:
ROMs: roms/<system name>
Collections: configs/all/retrofe/collections/<system name>
The corresponding local paths are:
ROMs: ~/RetroPie/roms/<system name>
Collections: /opt/retropie/supplementary/retrofe/collections/<system name>