Where/how do I enter the Medicare Part B premiums under my self-employed business instead of under SSA-1099 section? Where is the box for self-employed health insurance?

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Yes, if you are self-employed and eligible for the self-employed health insurance deduction, you can include your Medicare premiums in your self-employed health insurance deduction. It's a deduction on the front page of the 1040, line 29.  

If you want these premiums to be part of the self-employed health insurance deduction, do not enter your Medicare premiums when entering the information from your SSA-1099 (Social Security Benefits). When you go through the questions for your business expenses, enter those premium expenses for self-employed health insurance premiums.