Try this first
http://gbatemp.net/index.php?showtopic=92269&hl=
Will probably help us understand what you clicked, so walk us through what you do. We can tell you what you did wrong.
Remember to use the U8 Extractor, select your 5.app file in the top and select a folder on the bottom. Screen shots will help

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Edit: Also if your doing this to EBZero, I did too... your gonna have one hell of a time. Apply Tomatos update patch. While the game was charming, it still required a lot of leveling up, and had a HUGE map with a VERY high encounter rate. If you really want to play it, and play it quickly, but still feel like you got the experience from the game, my suggestion is to hack it.
If your comfortable hex editing, head over to the
EB-0 Data Crystal Page
I set my encounter rates to 1/3 that of the original.
On to the enemy data. I set a few select enemies to give me 65536 exp. That way I could return to them and level up my allies.
Those few things made the game MUCH more enjoyable. No grinding, much less interruption, and less frustration on my part.
Test these on an emulator before injecting to make sure
. If you max out the Doll's EXP you can be at level 60 or so by the time you leave the house.