[Stilgar]

You need to find an item that can be upgraded (lightsaber, prototypevibroblade etc)
And an item to upgrade it with (Vibration Cell, sabercrystal etc.)

Then go to the workbench, and click on the type of item you want to upgrade, then click on the item you want to upgrade.

Then you will see 4 slots for swords and blasters, 2 if you clicked armor, and 3 if you chose lightsaber.

If you have somthing to upgrade the item with it's slot is highlighted and when you move your mouse over it it sais what the upgrade does.

Click it, and the item will fill the empty slot (you see the item in the slot)
Then click assemble and your item is upgraded.

To remove items do the same only click to remove them (don't forget to click assemble again to permanently remove it)

Good luck