They should have issued you a 1099Misc for what they actually paid you, the $6,000.
It is very difficult however to get companies to reissue the 1099's (which they should do), so report the total 1099Misc amount and deduct the $2,000 as a supply expense.
IRS matches these documents to the return so if not reissued, they will be looking for the $8,000 on your return when they match up these documents.