One way you can use UnrealPak.exe to packagin is
%UnrealPak% %PakFilename% -create=%ResponseFile%
where is the path of UnrealPak.exe, %PakFilename% is the path of the pak to create and %ResponseFile% can be the path of a .txt file which contains the list of files to package. But this txt file needs to have a format, here is an example
“D:\MyProject\PakAdmin\ExtractedData\MyProject\MyProject.uproject” “…/…/…/MyProject/MyProject.uproject” -compress
“D:\MyProject\PakAdmin\ExtractedData\Engine\Content\Slate\Testing\Wireframe.png” “…/…/…/Engine/Content/Slate/Testing/Wireframe.png” -compress
“D:\MyProject\PakAdmin\ExtractedData\MyProject\Content\Art\Sounds\SND_Card_Tap.ubulk” “…/…/…/MyProject/Content/Art/Sounds/SND_Card_Tap.ubulk” -compress
You can see that the left side is the file location and the right side is the mount point of each file