How to record inventory payments vs tracking inventory

If you are a manufacturing company, your transactions would be mixed up between raw materials (AP transactions) and inventories (AR transactions). QBO doesn't offer any feature to manage raw materials. Consider having an additional app to do so and integrate it with your QBO account.

First, make sure that your inventory items have both a revenue (sales) account and a CGOS account in the product set-up.  When you buy inventory, use a Purchase Order with a material receiving transaction (this preserves FIFO accounting). 

Second, Pay the PO bill via credit card but applied to the PO, otherwise the expense gets doubled.  

Check your past transactions and you can see which accounts were expensed and how the condition happened.  If it's a manageable number and timeframe, you make be able to adjust this before year end.

Best,

Kevin