If all of the self-employment income is reported on a single Schedule C enter the entire SEP contribution. If you've created separate Schedules C for your separate businesses, made the maximum SEP contribution based on the combined profit and are claiming the self-employed health insurance deduction with respect to the business that produced 95%+ of the profit, enter only 95%+ of your SEP contribution.
(With sufficient net profit, it probably doesn't matter what you enter. If entering 100% of your SEP contribution does not limit your self-employed health insurance deduction to less than the amount of your insurance premiums, you can just enter 100% of your SEP contribution.)
