I have a very simmular setup in my house. I have a pan in the return duct under the coils that has a switch, but no drain. The pump has a switch in it connected to the unit that will shut off the unit incase the pump fails. The short chunk of PVC that sticks up is for adding clorox once a month to kill all the gunk, and keep the pump from getting cloged. Mine has a PVC cap over the pipe, But I dont think it would matter if it were missing.