you must create a separate folder called levels, put the folder of your map in there so you have levels/$YOURMAP, then zip it and you're done!
Would i get my custom map file in /levels or in /mods/repo? i tried unpacking and packing the map file in beamng then copied it to a laptop to make sure it works i seen the map in the free roam area but when the car spawns in there is nothing. --- Post updated --- this is the folder.
Did you start your custom map from a vanilla map or another modded map? Then only your changes are in your levels folder.