Uhm, haven't used it in a while, but iirc:
- Fire up DayZ Commander and connect to a server running the map you want to edit.
- Before it actually logs into that server, go back to main menu. It was just an easier way to start the game with a specific mod.
- Hit ALT+E to open the map editor, the map you want to edit will be in the list, quite possibly with an icon or something like that next to the name.
- Place a Center (dont change any values in the little window that opens up), a Group (dont change any values in the little window that opens up), and then a Unit (set 'Playable' to the Playable value, set the skin to survivor or s.th. if you want, doesn't really matter tho. Just the playable part matters) to the map anywhere. ArmA2 Map Editor doesn't let you save it otherwise.
- Place objects via the Vehicle (most objects count as vehicles, just roll with it. Don't try to place actual vehicles like cars or helis this way. It doesn't end well!!) or Object Composition button, then save to a name.
- Leave the editor, alt+tab out of the game.
- Open your %USERS%/Documents/ArmA 2 Other Profiles/%profile name%/missions/ folder and you'll see a subdirectory named <the name you used when saving>.<name of the actual map>. In it is a .sqf and a .biedi file, drag&drop the .biedi file onto 3de_conv.exe (look for 3de on one of those arma2 mod sites, you'll find it), it creates an sqm file.
- Open your %USERS%/Documents/ArmA 2 Other Profiles/%profile name%/MPMissions/ folder. Create two folders, one named original.<mapname> or s.th. like that and one named <whateveryouwant>.<mapname>
- Put the .sqm file 3de just created into the whateveryouwant folder, grab the MP mission pbo for that map from your server, create a backup of it, open it up in PBO manager (you'll find it anywhere 3de is available too), and drag&drop the contained .sqm file to the original.<mapname> folder
- Alt+tab back into the game. Go to multiplayer, chose the New button to create a server and hit ok to get to map selection, select the map you edited from the list at the bottom, then select <<New - Editor>> on the right side. It will open up the editor again. Click on load, the dropdown should show both the original and your version. Load the original.
- Click on merge, select your custom version from the dropdown. Find the blue Unit thing you placed earlier. Select it and delete it, we can't have that there, we only needed it because of a restraint in the editor earlier.
- Click on save, enter a new, third name of your liking, exit the editor and cancel starting up a server, leave the game altogether.
- Open your %USERS%/Documents/ArmA 2 Other Profiles/%profile name%/MPMissions/ folder. There is a third folder now, <thirdnameyouused>.<mapname>, in it is a .sqm file. Open your pbo file from earlier - remember to keep a backup of that file somewhere - remove the sqm inside it and copy over the mission.sqm from that third MPMissions folder. Close the PBO and replace the one on your server with that new one.
Done.