If you install a newer version on top of another version, the software will automaticly put all of your files into a folder called 'Windows.old'. This is where you can find all of your previous files.
If you just upgrade to ultimate, it won't change, it won't delete your files. But to be safe, make a backup copy in case something goes wrong.
Another tip:
Devide your HDD's into partitions where you keep like 30 to 50 Gigs just for system use only. this way system files don't get corrupted as easily.
I installed Home premium on top of XP, Ultimate 64 on top of ultimate 32, ultimate on top of home premium, etc.. it always puts my files into Windows.old folder. Or when you have a Windows.old it makes a folder: Windows.old0000 etc.. So the chance of you losing your files is quite small, unless something goes wrong during installation an your HDD fails.