Hi Paul,
Are you referring to using ArcSDE service connections to connect to your geodatabase (either version 10.0 or 9.3.1) on SQL Server 2005? You can do it that way, the direct connections are the ones that have issues to SQL Server 2005 with a 10.0 or 9.3.1 geodatabase. But setting up an ArcSDE service connection at 10.2.x is all done manually now.
Using ArcSDE service connections @ 10.2
Creating an ArcSDE service @ 10.2