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There is no way to turn the fans RPM down (there is but not worth it) I have my PS3 up right and I have no problems with noise only when the drive is reading a disk.
Just make sure it is well ventilated and if possible standing up right and not lying down.
To be honest with you I done really know, I am only quoting what others have said in the past.
I think its to do with the way heat is vented out, so if its standing up, only the vent at the top gets hot where as when its lying down the whole of the top get hot making the fans spin faster?