Open the Toolset.
Open the JEGs .mod file. It'll take a few minutes to load.
To check the .hak files loaded, go View (pull-down) --> Module Properties. In the Module Properties window (usually on the upper right of the app, click the Properties tab, then look down about 4 lines to the Hak Paks row. Click on the button on the right of the list in the second column, and you'll get access to the Collection, where you can manually add .haks. Check the list, then add what you're missing.
I had to do this myself recently, so it's fresh in my mind.

As J.G. Ballard has said, "It's a mistake to hold back and refuse to accept one's own nature."