A.D. did steal Emily's eggs. But to have someone's eggs inserted to another female will require some type of fertilization (aka surgery). Plus why would Archer or A.D. care to put Emily's eggs in Alison? When A.D. left that note that said something like "you better talk before our baby talks", I think he was referring specifically about him and Emily.
Plus, if A.D. wanted Alison pregnant, why not just do the simple dirty work? (Archer's sperm + Ali's eggs)
Well, A.D. is probably holding Emily's eggs hostage as long as she is keeping any secrets that could help reveal who Charlotte's killer is.
Putting Emily's eggs into Alison is a little gross and pointless to an extant. If A.D. wanted a baby out of Alison why not just do the simple dirty work (Archer + Ali). Why have Emily's eggs and not hers?