Here is a technique for encapsulating a nut with in your part design.

Edit the Gcode file at the level where the pocket starts to be closed (you can use notepad to do the edit and just search for the Z axis move that is taller than the nut pocket)

Just before making that height move, insert an x axis move to get the hotend out of the way

Example:
G1 x****** F1800.00 (a number big enough to give you room to work
G4 P1000000 Pauses the program long enough for you to insert the nut)

The program will restart after the pause period and seal in the nut.