if you are using AE 7 read no further.., if under that version AE will not read native maya files (iffs) unless you open and change 'all recognisable files' to 'all files' and then tick the force sequence box (bit rusty on 6.5 but you will see what I mean) as far as the alpha.., just press 'best guess' when the files open
take it easy and life will be easy