I asked this same thing previously but it is kind of a manual process that I
chose. You can use the apply order in the Wat list at the top but if you have
2 orders with the same part you can accidently apply some parts twice if you
are not careful.
I ended up using BrickStore which is a free program that connects to Bricklink.
I download my orders and then sort by part number. Once I have this I go to the
Search in the Want List menu and search for that part. Then, I can compare the
numbers and update the have quantities.