Tim, Im no expert thats for sure. you need to be working in 32 bit, thats 8 bits each for RGB and another 8 bits for alpha. on import you should have an option box come up (in After effects) that asks if you want to ignore the alpha ( other questions too but you know what they are). should be no problem??
this must be a maya question, how to get alpha tiffs out of maya?? after effects shouldn't give you grief. if so let us know. all I can suggest is look at the help files (if this is a maya question) other than that have you looked at the stacking order of your layers?? the alpha lays on top (I think?? Id have to go in and have a look, some things we do end up becoming automatic or juist 'do this and see what happens')
not enough info here for me (not that I think I could help much but one never knows)
Steve and me must have been witting at the same time.
take it easy and life will be easy