Welcome mate! Firstly, have a really good look around here as this forum has tons of info and virtually everything you will do has been done by one of us lot and documented here somewhere. Also have a good look through the Administration Guide - http://na.blackberry.com/eng/deliver...tion_Guide.pdf
For upgrading I would suggest the following -
1. Get to grips with the current setup and document everything asap
2. Find out where your support is coming from (you will either be paying RIM for T-Support or you will be getting it from your carrier, hopefully)
3. Make sure the BES db is being backed up once a day at the very least, as that is the heart and soul of the setup
4. Once you are happy with what you have, upgrade to the latest SP and MR based on the docs from RIM (the SP will have a doc telling you what to do and how).
5. Once you are running fine with that, make sure your management know that 4.0 is end of life and start planning to upgrade to 4.1 (Voda don't support 4.0 anymore so bring that to their attention asap if Voda are providing your support). If you have T-Support you will probably get it gratis but if not the cost is small compared to the funky stuff you gain with 4.1 (not to mention being supported again!!!!)