QuickBooks is usually versatile enough to not only handle your specialized accounting needs, but to be able to handle those needs in the way you want. A great example of this was recently discussed at CPA911.
The post looked at setting up QuickBooks Inventory Adjustment accounts. While QuickBooks automatically sets up one of these accounts in your Expense section, you might prefer to move it to the Cost of Good Sold section in your chart of accounts.
If you’d like to set up your Inventory Adjustment Posting accounts this way, give the link a look. They also discuss a number of other issues related to Inventory Adjustments.