Repeating my answer from Discord, in case others with the same question find this thread:
Typically you’d have the sewer area and ground area as separate maps, and have Objects representing outgoing doors/warps in each one that specify where to teleport the player.
Less commonly, you might put each area as separate layer groups within a single map. This is sometimes more convenient for situations where you have a bunch of areas that all occupy the same horizontal space, such as the many floors of a narrow tower. The warps in this case don’t move the player to another map, but tell the game to show a different set of layers and use different collision. Since this is only really suitable for confined “vertical” areas, even if you use this approach, you’ll likely use the approach above for other areas.
What exactly the warp/door Objects contain is up to you, and depends on how you intend to deal with warps/doors in your game.
It could contain just a map ID, with the destination map deciding where to place the player (based on game progress, previous map, etc), or it could also define where in the map the player will spawn. The downside to the latter approach is that if you rearrange things in one map, you may need to update the warp(s) in other maps.
Some people define both outgoing warps/doors and objects for the spawn points corresponding to those warps. This allows moving the exact destination without needing to update other maps, but has the downside that when first setting up the warps, you’ll need to edit two maps. So, it really depends on what you need in your game, and your workflow.
For what it’s worth, in my own games, I define warps with a destination map name, and where the player will spawn in that map, which can be an absolute location, or relative to their current location, separately in x and y, so I can have one absolute coordinate and one relative. This allows me to mark the whole side of a map as a giant warp going to the adjacent map, which is handy for large interconnected areas. Or I can make a single small door that warps to a specific absolute location in the destination map, which is more appropriate for something like a ladder into a sewer.