How do I process a one time paycheck to myself for my S-Corp?

This is not compliant with the IRS: "I want to pay myself $6k salary and $6k bonus to and be compliant with IRS. "

You cannot take the equal amount as Bonus and underpay yourself. To Comply = Market Based reasonable compensation for services performed.

"How do I do a 1 time payroll check. If I add myself as an employee and give myself $6k salary and try to run a payroll it is dividing that by 12 months and only trying to pay me a few hundred dollars?"

You don't Divide a 1-time check. It's that one check, already.  You need to meet with your own CPA, because if the IRS catches this, you will be facing penalty and interest. They will recharacterize the other $6k as attempting to evade payroll taxes. That isn't legal.

The pay period must be set at monthly. That is why it is dividing by 12.  Can't you overwrite the amount?

You are supposed to pay yourself a reasonable salary; which $12k is obviously not, if you worked full time in the business.