I just ran across a good article by Joyce Rosenberg advising small business owners on what to do about paying income taxes if you don’t have the funds.
1) If you have file an extension, then you still have to estimate your tax liability and report it to the government.
2) set up an installment payment plan with the IRS is a good option. If you are going to go that route, you will need to file Form 9465 and there is an administration fee of $105.
3) To prevent this from happening next year, work on better cash management and set aside for tax payments throughout the year.