I’ve been doing the following from the command line:
Engine/Binaries/Win64/UnrealPak.exe [path to the directory you want the pak in] -create=[path to a text file that lists the paths to the .uassets you want in the pak]
You can also make them from the editor by following the steps in this post:
http://www.tomlooman./add-mod-support-to-your-unreal-engine-4-game/