If you are using SWPM/sapinst for the export and import then R3load will be used. The exported content will be in DB independent format. You basically export the source system and create the target system with the export dump. With this approach you avoid the database upgrade task if the source system was on a lower release and the target will be on higher release.
I believe for MSSQL 2008 there is a requirement to have a specific BASIS patch level for the SAP systems. (Not quite sure)
Check these SAP notes.
1076022 - Release planning for Microsoft SQL Server 2008 (R2)
1152240 - Setting Up Microsoft SQL Server 2008 (R2)
Regards
RB