If you are doing an amended return after already filing the return with the $3,000 liability, I would only send in the $11 with the amendment.
Be aware, you may get a bill after 4/15 for the large amount, but do not pay it. There is a significant processing time for amended returns (8-10 weeks). However, the IRS gives you 120 days to "pay". The amendment will be accepted by that time and your account updated.
