In my experience (I've done about 20 OS upgrades , small compared to some), What I have done is this:
1. Install the new OS and manually delete the vendor.xml file.
2.Backup my data using Desktop Manager (DM)
3. Backup my data using BlackBerry Swiss Army Knife (BBSAK)
4. Wipe my device using BBSAK.
5. Load the new OS using BBSAK. At this point I would select the modules that I wish to have installed on my BlackBerry (and I'm a minimalist)
6. Check all features and options of new OS.
7. Restore my data using DM.
8. Install my apps.
I believe each person would use a method that is appealing to them. My method for me is faster than using the DM to do the process. I get the OS wiped and installed much faster with BBSAK than using DM.
I do a double backup, because, well you never know.
Hope this helps