TO DDRPIP: Make sure you go to the part in the game that you want to retexture, because it only dumps textures from the game as they are loaded, so you can't just you leave it at the start screen and walk off for an hour and think that its going to have dumped all the textures in the game. I like it that way though, it makes it easier to know what part of the game the textures came from.
A lot of times things are made up of combined textures, and you just have to deal with it. To figure out where they go just paint numbers on them and different colors, that's how I mapped out the sky which had like 51 combined little textures, because I'm planning on retexturing it later, that's also how I figure out where textures are used in the game if I'm not for sure. If your making hi res textures that look exactly like the original but just better then you don't always have to map it out, like you wouldn't have to on the sky, just do each texture high res. I'm wanting to put a floating pyarmid in the sky with clouds around it sometime, so I needed to map the sky. Mode 7 just told me a good way to work with the many textures that combine to form something, such as the sky, but you'll still have to find out where they go, but it's easier to paint or create new ones because your working with all of them together like one pic instead of a 50 little pics that you combine.(It's in my thread called "check out my Super Mario textures").
To Vinilipe: So you know how to do dump and retexture properly and have been successful at it, and it's some more complex problem? I'm very new at this so I don't know a ton, but go ahead and describe a little bit about the problem and what your trying to retexture.