Here's my workflow and some tips:
- All my mission folders / repositories are in My Documents\Arma 3 - Other Profiles\AgentRev\missions, so they can be loaded in the editor quite easily.
- I create symbolic links from the mission folders I work on in MPMissions from the game's install folder, so they can be chosen in the mission list when you create a multiplayer lobby ingame.
- I set #define DEBUG to true in init.sqf, which causes custom functions to be recompiled from the files everytime they are called. This causes a 20-ish FPS drop, but you don't have to restart the mission just to test minor changes. I forgot a couple times to disable it before packaging updates

- I test the mission inside a LAN lobby created via Multiplayer > Host Server. If you change stuff that requires a restart to test (like the init.sqf or world saving load script), you can just go back to the lobby to restart the mission.
- If you change stuff in description.ext and/or anything relating to GUI config, you have to go back to the mission selection list before restarting the mission, which is just before the lobby.
- The game locks write access to files when they are being compiled or execVM'd. So if you have a file that is getting called often (like addAction scripts), you might get read-only warnings if you try to edit them. addAction scripts in particular can be paused by opening the Esc menu. Otherwise, you have to wait for their execution to be completed before editing them, or go back to the lobby and do the edits.
- Once you are ready to deploy an update, just create a PBO from the mission folder like normally.
- Like PBOs, all mission folders have to be suffixed with ".Altis" or ".Stratis" to be available ingame.
Hope it helps.