If you are an S-Corporation, as an owner(shareholder), you should be paying yourself a wage. For state/local tax purposes you are likely to be exempt from state unemployment and worker's comp. since these entities disregard owners as employees.  For federal taxes however, you must still make your 941 filings and payments, even if the only employees are shareholders.

Now about the SEP IRA contribution: Since QBO does not support SEP IRAs (though it DOES support SARSEPs set up before 1997 - see page 7 of IRS pub 560 for the difference) through payroll, you will need to make two journal entries: One increasing he IRA fund (set it up as a Banking account of type trust) and decreasing the business checking account (or recording the means of payment if not from business checking), and one journal entry debiting retirement plan expense and crediting retirement plan liability.