I usually put all gda files into the addin's module/override folder, unless it must be in the addin's core/override (I think I only have toolset_henchmenand the like in there, and I think rewards goes in there.) Be careful with the core/override files, they overrite anything with the same IDs (so don't override campaign IDs unless you expect players to uninstall your mod when not playing it.)
Unfortunately, the toolset cannot keep track of your gda files at all times. If you don't want to restart, I use all the palatte refreshes (three different refreshes from right-clicking in the palatte) and File->Restore Environment. I'm not sure which one does the trick, but I think it's "Refresh Override" that actually does anything. I'm just needlessly thorough.
Once the files are in the proper folder and you've restarted the toolset or refreshed the override, you should see the effects in the toolset unless something is being overriden.