Perhaps you found the answer for this, but this is in case someone else is looking:
The way I imported the Quantity on Hand is via the Physical Inventories under Warehousing. 1- I exported the products that I want to update in order to get the product external id and unit of measure. 2- Exported the physical inventories in order to get the format of the CSV file. 3- Copied the Product External ID and UOM External ID from the Products file and insert them in the CSV file to import 4- change the quantities (note that the quantity you set is added to the existing quantities, not replaced, i.e. stock move in) 5- Import the CSV file, Confirm, then Validate.
Good luck.
Did you ever resolve this? I was wondering the same thing.
I had this same exact problem so I figured a way to hack the quantities in. I am not sure if this will work for you, but here's the guide I wrote: https://docs.google.com/document/d/1ca9s836s5h1cnYttc2iCKkjjfFI4zjF93OPztAOzvU8/edit?usp=sharing