well, if you guys think about how Canti looks when he transforms-These square brainy things come out. I think his brain really is gone-and it's inside Canti. So, when Naota fights inside Canti, that is the only time that he's aquainted with his brain-which explains how he can fight good. I believe those X-rays are real. But, in that case, i don't really know if you can see a brain in an X-ray. I suppose you could, because it is pretty thick. So ya, there's no brain.
Then, in the last episode, the terminal core eats Naota's brain. Later, the terminal core eats Naota. I think this is how he got his brain back. He aquired his brain, and Atmosk's power.
hmm...i've just come into something else! yes, it's a little tid-bit moral thingy! lookie:
the more time you spend away from your brain, the more you learn about yourself.
HA! eat that

i think 'away from your brain' could translate to 'away from the things around you'. But, in FLCL's case, it's a brain. 'away from the things around you' IS what it means, though. Just the brain for this case.