What do I file a subcontractors expenses under for materials they purchase that we reimburse them for so it shows in cost of materials on the CIS return?

Hello Sara55, 

Welcome to the Community page, 

So there will be an account already in Quickbooks for this in the chart of account for you.

If click on +new>expense>start typing in the category section-CIS suppliers- you will see the option to select called CIS suppliers and materials reimbursed to select.

You can put it against that account.