Meaning: that you'll first create e.g. the directories...
..and that you'll then mount your partitions to those dirs:
mount -v -o noatime /dev/sda7 /home/media
mount -v -o noatime /dev/sda8 /home/web
mount -v -o noatime /dev/sda9 /home/honey
The partitions are physical, the connections to the mountpoints are logical - not doing what you describe ("I'd like this mounted as a separate partition") is impossible, so you're fine.
Concerning the rest, you have to dig into the "Plex" docs - no clue how they handle their VMs. But at this point at least you have the space where to put those VMs on.