Both versions are exactly the same and thus totally compatible, you'll just have to make sure that Seekers of Adoulin installs to where-ever steam puts FFXI. I don't know exactly where that is but I assume it's just with all other steam games?
Alternatively, the installer may be a symbol of how horrible SE is at designing software for computers, and you'll want to make sure that FFXI is already where Seekers of Adoulin is predetermined to install to by moving the Playonline folder that contains FFXI et al. to Program Files.
Either way, it'll work with minimal fuss.