I apologize for the lack of explanation. Hopefully the following helps.
Step 1) Install Hal's DLL file and Empty World
Step 2) Enable DM via the console.
Step 3) Enable flight so you character stops falling.
Step 4) Enable edit mode via "bbb ee" command.
Step 5) Load desired prefab for editing via consolte command "prefab load <prefabname>"
Step 6) Press ESC, and disable physics via the corresponding check box.
Step 7) Begin adding/removing blocks and/or painting.
Step 8) Save the changes to your prefab via the console command "prefab save <prefabname>"
By following these steps, I never have to specify the coordinates of the prefab for exporting which saves me time. I could then open the saved prefab within your editor make changes there, and then load it back into the same empty world without having to open/close the gameworld.
In general, I use your editor to do macro editing (multiple rows/columns/layers of blocks + sleeper volumes) and do micro editing and painting within Hal's empty world.