Have 1099 Misc. Isn't there a way to reduce that income dollar for dollar with a SEP contribution that is entered as expense and not SEP?

Yes, but only to an allowable limit. The SEP contributions go on line 19 of the sch C. The program will tell you the maximum contribution you can make based on your circumstances and carry it to your business as a deduction.

About Schedule C (Form 1040), Profit or Loss from Business ... for form and instructions. See line 19 instructions for the deduction.

Here are the IRS SEP rules and more information.