How can I populate Box 2, Box 3, Box 4, or Box 6 on form 1099-MISC in Accounts Payable?

You can enter the amounts into the W2/1099 Preparer window to have it reported on the 1099-MISC.

Box 2 - Royalties
Box 3 - Other Income
Box 4 - Federal Income Tax Withheld
Box 6 - Medical and Health Care Payments

In Accounts Payable, use Tasks, Government eFile and Reporting, Form 1099 (USA). Complete the necessary information in the various windows. When you advance to the W2/1099 Preparer grid, you can enter amounts into the appropriate 1099 box(es) for your 1099 reporting.

Refer to How do I print or generate Form 1099 in Accounts Payable?