Hi, after a bit of discussion, it seems classifications as vatthu and as ayatana are simply two different ways to classify dhammas, in order to show their different aspects. So, classification by vatthu has to do with the physical base of arising. So both citta and cetasikas have the same physical base of arising, while the 5 senses of course each have their own. When it comes to ayatana classification, it has to do with how dhammas meet or associate together.
So, cetasikas are put in dhamma-ayatana together with subtle rupas and nibbana, because these are dhammas that can only be experienced through the mind-door (interestingly, cetasikas cannot arise without citta, subtle rupas can, while nibbana doesn't arise or cease at all, being unconditioned). Citta is put into mana-ayatana, because citta is basically the meeting point for experiencing so to speak (which is also why mana-ayatana is classified as internal ayatana, while dhamma-ayatana is classified as external ayatana in the internal/external classification). And the 5 sense organs and objects are put in their respective ayatanas, since they are experienced through the respective sense-door.
Some of the related dsg discussion posts:http://groups.yahoo.com/group/dhammastu ... age/111562http://groups.yahoo.com/group/dhammastu ... age/112197http://groups.yahoo.com/group/dhammastu ... ges/112359