are you using the dual emunand setup, or just Rxtools and PBT, if so you should be able to backup all your saves from pbt using SDF, then use gateway straight from there with your current emunand, install all the games from sysnand and re-import the saves and just use all content in emunand as normal
Depends on how you do it. If you create a new emuNAND with sysNAND on the SD card where you have your content installed, you will have all that content. If instead you chose to keep your current emuNAND and use it with gateway, you keep all the stuff you have on said emuNAND.
However, if both sysNAND and emuNAND are linked, it does not matter.
Should be able to just use hex workshop, read from drive with offset one. Then use emuNAND tool to inject it into an emuNAND partition made by Gateway. Backup the SD contents beforehand (Nintendo 3ds folder) and then copy it back over when you are done.
