Good to hear that you enjoyed the game so far.
Way how to package a crate of Vortex is you open your inventory, if there is a bottle of Vortex in there, you pick it, then you use it on the cargo terminal.
As a result a full crate of Vortex will be added to your cargo.
This only works if you have six bottles of Vortex in your inventory, of course, because one crate will hold six bottles.