That's easy,I'll try to explain as best as I can
Once you have your mod loaded and set to the active file,go to the container section.
Then select a container of your choice (footlocker,sunset sas box etc)
I usually pick the Footloockerempty01 as it is the smallest one and doesn't look that ugly,but thats up to you.
Then rightclick it and go to edit,edit the base Id so no other Footloockers are changed as well.(if asked to creat a new form say yes)
Do not close the container menu,now go to the weapons section/or wherever your modded items are located and drag them into the "item list" of the container menu.
Close the container menu.
Now open up the cell where you want to place the box and it is done
Just do not forget to save your plugin