apt says it has vorbis-tools as a dependency, both the site description and the manpage says it uses oggenc, and the configuration file lists "oggenc" as the command name, but without the full path (editing it appears to be pointless, as it overwrites it every time). That means certainly that it uses the first instance of oggenc found in the PATH, which is usually the one in /usr/bin. Unless you have multiple oggenc versions installed and want to specify a particular one, I'd say you're safe.
I personally found the program to be too simple for my tastes. There's no way to edit the per-track metadata. I prefer using audex myself. grip isn't bad either, if you need a gtk-based program. There are other options as well; I suggest trying out different ones until you find the one that satisfies you.