I've been tasked with migrating our current SCCM 2012 R2 (CU1) install from a server running Server 2008 R2 with SQL 2008 R2 to a new one running Server 2012 R2 with SQL Server 2012 SP2.  I've got the basics understood of restoring SCCM to the new server but what I'm unsure of is whether I can use the SCCM 2012 R2 SP1 install media on the new server and point it at the backup from the SCCM 2012 R2 (CU1) server to restore to the new server or do I have to use the R2 media and then upgrade to R2 SP1 after the restore has completed?

I'd go with the original R2 media and do the upgrade to R2 SP1 after the restoration is completed.

You have to use the "media" that matches the version of the backup. The restore wizard will complain if they do not match.