What I generally do with a corrupter is wipe one chunk at a time to the value 0x20 and see what it does. Using 0x20 makes the effects usually fairly obvious; e.g. you can quickly tell if you've wiped out graphics, TSA, or level data. Using random values is not recommended since you won't be able to reproduce the effects as easily. Usually the chunks are entire ROM banks but if that doesn't work then I cut the size in half and try again (though this has never actually happened.)
Every time I wipe out a section I write down its address and what happened. Once I find something interesting, such as the game freezing on a specific level, I narrow it down - wipe out only the first half of that area and see if it's still acting strange. If so, wipe out just the first half of that half; if not, try the other half. Keep narrowing it down like this until you have a very small area, and then you can try to figure out the format of the data you just found.
If you go through the entire ROM and nothing stands out as particularly interesting, go back and start narrowing down anything that seems to be related. E.g. if all you managed to do was crash the game when it loads any level, start looking at those sections.
It can speed things up a bit if you quickly go through the ROM in a hex or tile editor and make note of all the big empty spots, so you can skip trying them. (And keep that list, you'll probably want free space later.
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