I would sugges checking out the Handhled Management guide from www.blackberry.com
for some good information on how to deploy handheld code.
Basically, you are going to need to push desktopmanager 4.0 to the machines however you see fit then get the right device software on the devices. There are a few ways you can do it. If you have the bandwidth, one of the slickest wasy is using application loader lite. basically, you put all the device code on a share on your network as well as the loader.exe file. You would then just send you users a link yo the loader.exe and have them run it while the device is connected to the pc and it will load the 4.0 software on the device.
There is some set up you need to do to make this work so I suggest you get the Handheld Management guide from RIM. It will give you all the info you need.