This tutorial tells you how to edit the acres themselves. You know, the layout. You can make it completely look different! This will not focus on any sprites on the map, as that's coded separately (and honestly, I haven't figured out how that works yet).
Oh yeah, and to figure this out, you also need to know how hex works, and how to multiply and add using hex.
So first, you want to know what acre you want to edit. To know this, you first need to know which location it is in (example: the overworld map, Toronko Village Water Station, etc.) There is a starting offset depending on which location the acre is in (I had to figure this all out by trial and error):
* 18C000 -> Ion Island Cave
* 190000 -> Marts & Houses, Burion Relic: Floors 7-9, Human World
* 194000 -> Burion Relic: Floors 1-6
* 198000 -> Kakotos Relic
* 1A0000 -> Overworld Map (Top-left, top-right, and bottom-left quadrants), Antenna trees (same quadrants)
* 1A4000 -> Overworld Map (Bottom-right quadrant), Antenna trees (Bottom-right quadrant), Toronko Village Water Station, Kurinon Village Cave, Paparuna Lake Laboratory, Panses Village Cave
* 1A8000 -> Toripa Antenna Tree Cave, Peperi Mountain
You'll notice that a couple of locations are in different banks. For example, the bottom-right quadrant of the overworld is in a different place, and Burion Relic is also broken up too. You'll also notice that 19C000 has no starting offset. This is because this is where the game's maps and warps are stored, among other things.
Keep this starting offset in mind, as you'll need it later.
Second, you need to find the hex value of the acre you want to modify. You can do this with two ways:
1. Go to the acre, then use the Memory Viewer to look up address 0xC903. This is the simpler method, but it may be more time consuming because it may take a while to get there.
2. Locate the position that the acre is on the map. Find the coordinate of it. Then, look in the ROM and find the map of the acre you want to modify. For offsets, click here. Once you find the offset for this, then locate the coordinate of it in the ROM (it goes from left to right, then from top to bottom, it's always 8x8). You'll get your hex value here.
3. Here is where you need to do some math. It REALLY helps if you have a calculator that can do hexadecimal. The Windows calculator can calculate in Hex in scientific mode. Now take this value that you just obtained, multiply it by hex 50 (this is 80 in decimal), then add this to the starting offset you find a while ago.
4. This is where the data for the acre you're modifying starts. Conveniently, the format is completely uncompressed (unlike games like Super Mario Bros., where it uses an annoying compressed format). This means that each byte is a 16x16-pixel tile. The data goes from left to right, then top to bottom. There are 10 16x16-pixel tiles in a row, and 8 in a column, resulting in 80 bytes for each acre. (Remember, the status bar takes up 16 rows of pixels, resulting in a smaller screen). And because of this, the offset where the acre data ends is hex 4F (79 in decimal) bytes after it starts.
5. Each map uses a different tileset. In these images I made, it goes from left to right, then top to bottom. Here are tilesets for all the maps (note that for most of them, many of them are just glitch tiles, and lots are unused):
Overworld
Antenna Trees
Toronko Village Water Station & Kurinon Village Cave
Houses & Marts
Paparuna Lake Laboratory, Panses Village Cave, and Ion Island Cave
Toripa Antenna Tree Cave
Peperi Mountain
Kakotos Relic
Burion Relic
Human World - Main Area
Human World - Antenna Tree
Human World - Unused Buildings
So just play around with it, and see what you can come up with!
One thing you'll notice is that in almost every map, there are a couple or so tiles that look graphically identical to each other (for example, tiles 11 and 86 in the overworld). Even though they LOOK the same, they're functionally different. Often, the first one of its kind is NOT warpable, while the second one (which is usually way after the first one) IS warpable. However, I have no idea why sometimes there are identical-looking doors.
Confused? Well, I'll do one example. Let's do the very first place in the overworld:

First, you have to find the starting offset. Looking at the list way above, you'll see that the bottom-left quadrant of the overworld starts at 1A0000. You'll need this for later.
You need to identify where this is on the map. I've said this many times, but the overworld map is really four smaller maps joined together. So we're only worried about the bottom-left part. Now looking at it, you'll see that this is in the 5th column in the 3rd row:

Now we have to find the map data. Using the link on DataCrystal, you'll see that the data for the bottom-left quadrant of the overworld is found from 19C50E-19C54D. That's the data we want:
80 81 82 83 84 85 86 87
88 89 8A 8B 8C 8D 8E 8F
90 91 92 93 94 95 96 97
98 99 9A 9B 9C 9D 9E 9F
A0 A1 A2 A3 A4 A5 A6 A7
A8 A9 AA AB AC AD AE AF
B0 B1 B2 B3 B4 B5 B6 B7
B8 B9 BA BB BC BD BE BF
Now look at the data, and find the 5th column in the 3rd row. You'll see that it's 94. This is the hex value of the acre that we need.
Now that we have it, we need to use this to find the offset of the acre. First, multiply hex 94 by hex 50, and you'll get 2E40. Add this to the starting offset that you obtained before (1A0000) and you get 1A2E40. Bingo! This is where the data for the starting acre starts. It ends at this offset plus hex 4F, which is 1A2E8F. So the data is from 1A2E40-1A2E8F.
Time for the fun part. Here is the data for the acre:
04 03 04 17 92 92 17 03 04 03
15 11 11 11 11 11 11 11 11 01
15 11 11 11 11 11 11 11 11 03
18 0F 19 11 11 11 11 01 02 01
0E 91 0E 11 11 11 11 03 04 03
11 11 11 11 11 11 17 87 9A 01
11 11 11 11 11 11 11 88 11 03
02 01 02 01 02 01 02 01 02 01
If you look at it carefully, doesn't it look like the acre itself? Yes it does! Let's compare it again:

How convenient!! That means one byte equals one 16x16 tile. For reference, don't forget that this is the tileset for the overworld:
http://img98.imageshack.us/my.php?image=tiles04bb7.gif
While playing around, I changed it to this (of course, you can do whatever you want):
04 03 04 17 92 92 17 03 04 03
15 15 15 11 11 11 15 15 15 01
15 11 11 11 11 11 11 11 15 03
18 0F 19 11 39 5E 1C 5E 5F 2D
0E 91 0E 11 39 0A 1C 0A 0A 2F
15 11 11 11 39 0A 1C 87 9A 01
15 15 15 11 39 0A 1C 88 11 03
02 01 02 01 02 2B 02 01 02 01
And what did I get? This!

Totally awesome. I was kinda limited to what I can do, though. I had to keep the house where it was, or else it would have caused problems when starting the game (because the characters walk in a set path, which I don't know how to change). And I had to keep the treasure chest in the same spot, because if you move it somewhere else, you have to edit the treasure chest data, which is separate (and this will be my next tutorial). If you don't edit the treasure chest data, then the chest will be empty. And I had to keep the doors there, or else editing the warp data would have been quite a lot of work (though still doable).
Just try it out though -- it's really fun! (Hopefully you can do better than what I did...)
Oh, and I'd like to end this post with a proof-of-concept patch. This patch modifies the layout of Toronko Village Water Station -- every room looks at least somewhat different. Unfortunately, my lack of knowledge of editing sprites (both their position, and their set paths after talking to them, like the guy who rams into the locked door then runs off) limited me to what I can do, so it's not COMPLETELY different. But at least this patch can show you what can be done with it. And I figured out how to move the chest with the key in a different place without any problems, which I've been meaning to figure out for ages!