Make sure that you have the PKG files in the root of your USB drive, then navigate to the "Install Packages" option in the Game section of the XMB. Select the package you wish to install. IIRC each of those packages specifies which folder location you want to install your backed up games to, so you dont need to install both.
If you are still using the original PS Jailbreak Backup Manager, Gaia will not erase your backed up games. Use an FTP Client on your PC to move the game folders over the folder you choose for Gaia.