Now I do not know much about the AEM F/IC, but what you need is a translator of some sort; MAFT pro, HKS VPC, e-manage ultimate, etc. that will translate the signal from the MAP and IAT to a signal that the stock ECU can read as if it's using a AFM. If the device you are using is capable of a AFM delete or speed density then you will be good to go.
The MAP just runs off of a vacuum line, directly off the intake manifold gives you the most accurate readings. Then make sure your IAT is not going to be placed in an area where you will get a lot of heat soak, that will mess with your readings also.