Microsoft have finally after much community pressure documented the official downgrade path for those customers who have purchased SBS 2003 R2 Premium Edition and still need to run SQL 2000 due to application vendor compatibility issues. This is great news for us SBSers as it’s been a thorn in the side of many line of business applications that still (even 2 years after SQL 2005 has been released) do not support SQL 2005. Anyway congrats to Microsoft for listening and making this happen. The KB article is KB 935573 link below http://support.microsoft.com/kb/935573/en-us
Be warned though – you have until April 2008 to get this fulfilled and then the offer will be no more!!!!!