You can rework the game set-up screen to load a custom set-up page and the like, but this requires a lot more work, a re-written lua and xml file for the set-up screen, and perhaps more that I am not thinking of at the moment. They then select the map in Advanced Setup, click 'Back' once the map is selected, and then click on the little button called as I recall 'Play As Scenario' that would then show on the normal modded-game set-up screen.
Most people just add the map to the mod, set it's 'Import Into VFS' to 'false', and have the user copy the map from the mod to their ~\My Games\Sid Meier's Civilization 5\Maps folder.
