Most of your individual settings should be retained as they are stored in your /home folder. Open up a file browser such as Konqueror, select to view hidden files & you should see all the folders for each program.
I'm not sure what the exact procedure is for upgrading SuSE, but if you are only upgrading (instead of a new install), then it should retain the programs you already have on the / drive. If you decide to do a new install, then most likely SuSE will reformat the / drive & you will lose those programs & have to reinstall them. Your /home partition should still be retained.