I am sure everyone is asking a ton of questions. I have been asked to upgrade our BES server (previous admin did the install/config) I honestly don't know a whole lot about it. I am running Windows 2003 Server SBS SP2, with Exchange 2003 SP2 & SQL Server Desktop Engine all on one machine. (total of 2 users)

When I am asked about the upgrade type, how do I know if I am running the MDS Integration Service?

If I installed it with MDS Integration Service can I uninstall that feature only if not needed?

There's a 99% chance that you're not using MDS Services on your BES.
This is used by companies who develop and deploy their own custom Blackberry applications. If you're not doing that... then don't install MDS Services.

I have MDS installed, but we're not deploying custom BB apps.... yet. I didn't want to have to go back later and install it. Better to plan ahead than chase from behind.