When you work with Map Editor you see all the "special" tiles, but when you start a game the ones that are too far from land to be of any use (<2 tiles away) are not shown. This makes it a little harder to discern the patterns, but the original patterns are not disturbed.
The way I tell where things are, I start with a blank map in MapEditor and locate the tile where my settler(s) start. One of the coordinates needs to be halved (I'm not at my playing machine - I don't remember which one) due to a difference in the way Map Editor and the game program display the maps. Draw in the visible land, ignoring any Whale/Fish tiles that turn land into specials. Just get the correct land type down first. Then hit "S" and increment the Resource Seed till you get any visible specials in the right locations. If they and any visible huts are in the right locations but the wrong "type", add 16 to the Seed up to 3 times. One of these combinations should give you the correct Seed. If you have no visible specials or huts this is still useful info: try adjusting the Seed and record how many possible Seeds between 1 and 16 give you no visible specials or huts. You should come up with only one or two (x4 for multiples of 16), and those options should show something nearby that you can start your settler heading toward to confirm. Once you get the Seed right, you will know the patterns of specials and huts throughout the whole map. If you have Grass tiles at your start they could be "hiding" specials underneath them; in Map Editor I like to mark them with Tundra so I can see the hidden special.