I have some information to share with you, @km58256.
In accordance with the IRS, retirement plan contributions for a self-employed individual are deducted from Form 1040 and not from Schedule C. Please know that QuickBooks Self-Employed is designed for freelancers and it offers basic accounting. The categories available match with the Schedule C levels from the IRS.
You’ll want to reach out to your accountant to help you classify these contributions from the business account to your SEP account. They can assist you further and ensure everything is correct.
If you don't have one, you can visit our ProAdvisor website to find an expert. Our ProAdvisors are tested and recognized by Intuit, who can guide you further from technical and accounting perspectives. Just simply enter your city, state, or ZIP code.

These resources will provide more information about SEP and how it’s calculated:
If you have any other questions or concerns besides classifying contributions, please don't hesitate to let me know. I’ll be here. Always take care!