First, it sounds like your computer is running windows. Windows can only see the Boot folder because the retropie folder is formated ext3/ext4 and Windows has a hard time reading it(at least Windows 7 does). I can't help you much there. If you can find someone with a linux box you can take your sd card, put it in a reader and insert it into that box and you should be able to see the retropie folder as well.
You could download a raspian image to a separate sd card, boot up your pi with that and use your card reader to open the retropie folder on the RetroPie sd. First copy your new game roms onto the desktop of your new raspian bootup. Then plug in your RetroPie sd in your card reader and you should see the retropie folder. On your RetroPie sd you can mine down thru home, pi, RetroPie, roms and finally to the folder holding the roms for your games. Then you can drag-and-drop your new game roms into their proper place.
I hope this helps.