What about a tab-like extension to the side of the GUI, containing individual buttons for each group, named to whatever you want. Clicking the button enables all of the add-ons in that group.
Put "Edit" and "New" buttons at the top of the tab. The New button brings opens a replica of the add-ons GUI, except the presets area is replaced with a textbox for the name, a done button, a cancel button, and a clear button. Users select the add-ons they want in that group, type in a name, then click done. The new group then appears in the groups list. Editing would work by clicking the Edit button(which works in a color changing toggle style so you know if you're about to edit something and can go back to normal mode), and clicking the group you wish to edit. You are brought back to the replica Add-on gui, with the add-ons in the group already selected, and now with a delete button added to the possible options.
Removed due to not noticing that this is just for selecion purposes.