The first thing everyone wants to do after they root is uninstall the applications they dont use or want (bloatware) the problem with this is if you still want to run official ROMs from HTC you will not be able to install updates without those pre-installed applications. The solution is simple, dont uninstall just freeze. This is how you do that:
Install VISIONAry r14
install Titanium Backup
Now temp root your device with VISIONAry r14. Once you have temp root open up Titanium Backup. The first thing you need to do is click on the button Problems, this will install an updated version of BusyBox (you need this). Now click on Backup / Restore this will display all the installed applications on your device. Now find an application in the list you would like to freeze, tap it quickly a menu will pop up, select Freeze, do this with each app you no longer want to show up in your app tray.
Freezing an application keeps it from running, it is still installed but it will use no resources and it will not show up in your app tray. When an OTA update from HTC is pushed to your device all you have to do is defrost the frozen apps, install the update then refreeze. Easy as pie.
use EXTREME CAUTION when freezing apps, if you freeze the wrong item you will have a very expensive paper weight on your hands.
Below is a sample list of safe to freeze bloatware on the MT4G:
Mail 1.1.0 (if you do not use the HTC mail client)
Messenger (if you dont use Yahoo)
I think I finally figured out my question about this. You can temproot once with VISIONAry, do the steps, and then be done. You do not have to have VISIONAry set to the "temproot on boot" option that runs any time you reboot your phone, right?