http://gbatemp.net/index.php?showtopic=45360 if you fancy going manual (crystaltile2 has a few things that make it easier)
If you do go manual for whatever reason you will probably have to redo the header signing, there was a thread on that the other week (someone wanted to change the internal name) but you will have to look for that (I replied in it if you fancy going back through my posts).
I would suggest using DSBuff to edit the header info over RomeR since I had RomeR corrupt a game on me (RomeR crashed while editing the info and I couldn't fix it).
Additionally DSBuff does a bunch of other stuff, like unpacking the game so you can get to the individual files. You'll need to do this (then find and decompress the file) to edit the logo screen. You'll possibly end up using TileMolester to edit (or to export the image, edit and then import it back).
I'm pretty sure that this will vary game to game so there are no universal instructions.
Not what you seem to be expecting anyway.
Here's the "Game Over" graphic from LodeRunner:
To get it in a usable condition, I have to do a few things after opening the file:
1). View -> Codec -> 4bpp linear, reverse order
2). Image -> Canvas Size -> 8 Columns
3). Select the proper palette (I'm using a somewhat generic one)
4). Tile Forward to line up the image tiles (3 times)
5). Byte Forward to clean up the image (8 times)
And then I end up with this:
This is easy since none of the files I'm dealing with are compressed and can be viewed simply by using the correct settings.
If I need to edit the image I can either use TileMolester directly, or select a group of tiles and choose Edit -> Copy To... to export it as a PNG file. If you edit the image, you have to be careful to use colors that already exist in the image (or are a VERY close match) since they'll change to what is available when you put them back in with TileMolester.