When installing Backup Manager v2 it will ask you whether you want to overwrite the previous version chose yes and it'll install the new one and delete the old one. I believe the games do not delete and will stay there ready to use in the new backup manager.
If your original backup manager is referenced to save your games in game\LAUN12345\GAMEZ as in the original backup manager then yes, removing it will remove your games as it will remove that directory.
Your better off installing a backup manager where the games are installed in game\<name of your folder here>. Look in the thread entitled Backup Manager 2 as PSex submitted 3 versions that install in this directory, 1 uses a disk the second uses the ps3eboot menu and the 3rd without a disk.
As for your first question it really depends on the version you are trying to install as there are a few around that install in different directories.
Your best bet is to ftp over the GAMEZ directory to your PC and install a version that does not use the games directory and than ftp them back. That way you can install a later version or remove the existing version without having to worry about losing your games.