First of all, the transition has been a nightmare.
We have for the past 15 years used the Assembly of creating finished goods which are sold as a single item so that each time a product is sold each part of the finished good is subtracted from inventory. ex: A cleanser has a fill, a bottle, a pump, etc.
Now, with QBO is seems as though the assembly finished good does not hit the COGS with the cost of the parts. Am I doing something wrong or is QBO not capable of hitting all of the parts to COGS account?
All assembly parts BTW live in a program called SOS Inventory.
Normally, the Assembly items will turn into Bundle items in QuickBooks Online. This type of item doesn't have COGS since this is just similar to Group items in QuickBooks Desktop. However, the COGS account will remain in the inventory items, so they are still reported to COGS when you record sales for them.
The SOS Inventory you mean, I think that's the Inventory asset account assigned to your items. You can check that out by going to the Gear icon, choosing Products and Services, and hitting Edit onone of the inventory items in a bundle.
By the way, the Assembly is one of the limitations in QBO. You may want to check others here.
We're just right here if you need additional help, so please feel free to keep on posting questions.