For anyone who has never worked with hexagon tilemaps before (like me) and is looking to implement this in Godot as a tilemap, follow these steps (It's super easy):
1. Download the files and put them wherever you keep your projects assets.
2. Create a TileMap node.
3. Click "empty" next to tile set and select New TileSet. Then click "TileSet" where empty used to be.
4. Change the tile set shape to Hexagon.
5. Change the Tile Layout to "Diamond Down" (this makes the textures overlay correctly).
6. Set the tile offset axis to "Vertical Offset"
7. Set the tile size to X32 and Y28.
8. A the bottom of the editor you should see a bunch of tabs like "Output | Debugger (#) | Search Results | Audio | Animation | Shader Editor | TileSet | TileMap" -> Click TileSet
9. A little tab labeled "Tiles" should be selected with a big open space under it. Drag and drop your downloaded tilesheet of hexes into that area.
10. A pop up will say that the atlas's texture was modified and will ask if you want to automatically create tiles in the atlas. Click no.
11. Under the setup tab change the texture Region Size to X32 Y48
12. Now hold control and click to drag your mouse over all of the tiles. This will create the correct number of tiles with the correct sizes.
13. Click the tab above these settings that says "paint" and select "Texture Origin" from the drop down. Set the y value to 9, then click on a tile and drag your curser over every tile in the sheet to paint this value.
14. At the bottom, swap from "TileSet" to "TileMap."
15. Now select any of the tiles you want to paint onto your tile map and click into your scene to add them. You can use the drawing tools the same way that you would in a square tilemap. Enjoy!