Welcome to Smogon! Take a moment to read the Introduction to Smogon for a run-down on everything Smogon, and make sure you take some time to read the global rules.
Yes; If you want it to work, the 2 pokes used for the code MUST be in the first 2 slots of the party, and you must check the "Party Count" box and make it "2". Lol I have to go now, but I'll explain it more tommorow.