How do you set a continue point when making a dungeon with multiple floors?
Using the "Entrance/Exit" type warp will set a continue point. Using any other kind of warp ("Zap," "Insta," etc.) will not. Keep that in mind. I know it can seem useful to have multiple kinds of visual entrances, but the warp types do make a difference. For more information, consult the Wiki.
Is there a way to make a map that maps out all of the floors of the dungeon, and having a compass pinpoint a room on a different dmap, or floor?
.Level Numbers are the key here. The Map, Compass, Level-dependent keys, and Boss Key are applied to Level Numbers. Each Dmap can have only one level number, but more than one Dmap can have the same level number. Reserve level numbers 1 through 8 for those where you get a Triforce, and level 9 for the area where you use the Triforce pieces, just in case. Level 0 is always an overworld. At least as far as I'm aware.
So, if you want a dungeon with multiple floors (Likely meaning multiple Dmaps, each of which represents a different floor and has a different layout that depicts a different map layout.) but you only need to pick up the map or compass once in the entire dungeon, and be able to pick up keys anywhere in the entire dungeon that you can't bring outside of the dungeon itself, have all of the Dmaps use the same level number and make sure nothing else in the quest uses that level number. It's best to make a "Quest planner" text document that has a list of your level numbers and what dungeons use them. Believe me, it'll be -very- helpful.
Is there a way to "reverse," or swap the placement of pixels on the x-axis within a specific tile in the tile editor? Because that make custom enemies and bosses MUCH easier to do.
If I'm hearing what I think I might be hearing, you can horizontally flip tiles in the tile pages by pressing "h" on them to flip them vertically, and "v" (When you don't have anything on the clipboard, copied via "c") to flip them vertically.
The same thing is applied to combos in the combo pages or when editing a combo, FYI. Just know that tiles and combos can be flipped independently. You can flip a combo without flipping the tile it belongs to, but if you flip a tile in the tiles page, that tile is definitely flipped permanently. Though you can just flip it back just as easily.
You can also rotate tiles and combos with "R" - And rotate them the other way with [Shift]+[R]. The latter doesn't work in the combo editor but works in the tiles pages for some reason.