Actually, no matter where things get installed to, in the case of an OS re-install, you're likely to have to get a little work done to restore any existing data you want back.
More important than where software installs to, is where the software saves its data.
For instance, I may have a program installed in /usr like anything else, but saves the data to my home partition.
This is typical of any linux installation. So what you need to restore is not the program itself, but rather the data.
The program can be restored easily from a package (either created and backed up by yourself, or from the online repos)
After the program is restored, you can use it to restore the old data.
Hope this helps.