The big question for you (or anyone in this position) is are you actually using workspaces or mapping files?
SpatialDirect started out as a Mapping File only platform, so I won't assume you are even using workspaces. If not, then you could migrate mapping files (I believe) but you will want to schedule some time asap to investigate updating them to workspaces.
I'm not sure what database was in use in SD2008, but 2011 now defaults to Postgres I believe for the job management, etc, so there shouldn't be too much of a problem.
The best thing to do is check out the FME Server Administration Guide. It has a section on upgrading. You can find it on FMEpedia - look in the top-right for the link to the doc.
And if you do have problems, don't hesitate to contact the support team via http://fme.ly/support