you need to place your downloaded covers in '/dev_hdd0/game/MANAGUNZ0/USRDIR/covers' the image should have the front, spine and rear of the game cover you want. the image needs to be JPEG and a specific size (more on that later). To get Managunz to recognize the Game cover image it has to be named using the ISO format. For example: an image for 'ratchet and clank collection (USA)' would be renamed to 'BCUS98282.jpg'. If you don't know the ISO naming format for your game just google "xyz Game ID".
As for image size, through trial and error, I have found that 525x350 pixels is the perfect size and aspect ratio for PS2 Covers, and 525x270pixels works for PS3 covers. I have not been able to figure out how to get PS1 game covers to display in 3D yet, if someone knows that would be appreciated (250 pixel height works but I haven't figured out the correct width for ps1). If the images are too large Managunz will run out of memory and the game covers will start to look glitched. Personally I have roughly 40 backups all with ~100kb 3D game covers and it seems to work alright.
Edit: another trick that works is you can auto-download 2D game covers with Managunz, and it will name all the downloaded covers in ISO format for you. You can then simply open the auto downloaded image files one by one to figure out the Game ID's and just copy and rename files as necessary. I renamed all the 2D auto downloaded images as "xyz.JPGz" files so Managunz doesn't recognize them but they're still there in case I screw something up.