Ok ... still put the $6000 in the HSA and use the $6K (plus earnings) to pay the medical bills.
Putting $6K into the HSA is not like putting $9K in ... you are just saving $3K in taxes so you have $3K more in your pocket not $3K more in the HSA.
If you put $6K in the HSA you save federal + state + FICA taxes on that amount. So if you are in the 25% tax bracket + 3-10% state taxes + 7.65 FICA = 35.65 to 42.65% in taxes which will be reflected in your paycheck not in the HSA account.
