There is an Options button in Desktop Manager that you can click and it will give you the list of applications with all the check boxes.
Or even easier, don't use the full-blown Desktop Manager application for the install. Go into c:\program files\common files\research in motion\apploader and double click on Loader.exe (same program that is used w/in DM). I never use the full blown DM anymore - I only use loader.exe when doing upgrades.
Start loader.exe, then connect your BB. Can't miss the checked boxes.
No longer a BES Admin, but it was fun while it lasted!