Just add your scripts to the retropie menu, very simple. i never had to make any edits to make it work, just some editing to get the script to have a picture in EmulationStation and description of the script.
If you want the scripts to appear within your Ports, you might need to include .sh with the filetypes that are supported with Ports even though from memory it should already be set up like that (i cant double checking this right now, currently making a backup of my SSD)
If you can see the scripts in EmulationStation but theyre just not executing after selecting them, then you will need to chmod +x your sh files.