There's really nothing to separate per-se. When entering the rental income section simply select the option to indicate that some of the rental income was reported on a 1099-MISC, and some was not. Then enter the amount reported on the 1099-MISC, followed by the amount that was not reported on the 1099-MISC.
Understand that when you e-file the return only the total amount of rental income received is sent to the IRS. The fact that some was reported on a 1099-MISC and some was not, is not included in the e-filed return. Only the total amount of income received gets reported. That's all the IRS cares about.
You run into issues with the IRS if the total amount of rental income received does not match or exceed the total amount of rental income reported to you on 1099-MISC. In the case of a SEC8 rental the IRS fully expects the amount of rental income received to exceed the amount reported on the 1099-MISC.
