Not sure what you are doing just now, but the quickest way is -
1. Save your mod and keep the CK open
2. Start the launcher with only your mod enabled and click Play
3. On the skyrim load screen, open the console and type
coc yourcellname4. Run around your cell and see what needs fixed
5. Quit game
6. Make edits in your cell
7. Goto step 1
You cannot edit and save while the game is open because the .esp file is being used by the game.
[Edit]
Possibly another way is moving the coc marker around in the CK as well, so you don't have to run around to see your edits.