GE:S uses loadout script files to specify the composition of weaponsets and what gamemodes they should appear in.
Loadout scripts are stored in scripts/loadouts. Files that specify which loadouts a given gameplay should use start with gameplay_ and files that specify loadout compositions start with weapon_sets_
Open up weapon_sets_custom.txt in scripts/loadouts and follow the guide at the top of the file.
You can also make new files that start with weapon_sets_custom_ if you would like to keep things more organized.
The file that controls the weaponsets in rotation for a given gameplay will be called gameplay_GAMEPLAYNAME. For example, arsenal is gameplay_arsenal.
The three columns in this file are the weaponset name, weight, and grouping.
The name of the weaponset will be used to pull the weaponset from the existing weapon_sets_* files, and the weight and group will override whatever is specified for that weaponset in those files.
If a gamemode does not have a gameplay_* file, it will just use the default loadout settings specified for each loadout in the weapon_sets_* files.