When you say "air filter" do you mean air filters? on the N/A there are two filters, one one on each side of the engine cover/air filter box.

You do have to seat the rear of the box on the T.B. and make sure the it has sealed properly (rubber ring), then tap the front end down.

However, I'm not sure that alone would cause the check engine light on, have you read the codes yet to see what is not working correctly?