Well, it was flense both their necks, or give the Realio Trulio guy a perfectly-matching tattoo. But yes, the idea was that they would be indistinguishable, the cops would kill the wrong guy, and Ebil SK Mulder would go home and do Ebil Things to Scully.

I am led to believe that the whole thing with the Catzilla, the pint of Ben & Jerry's, the superheroic nanny, the latkes, and the later birth of twins sadly does not constitute Ebil; therefore, the plan failed.