Ok, I have an idea! It's passed over a lot and even I've done it before.
Note: I'm going by you edited your pokemon using the Party Edit panel.
There's 2 parts to it.
ON THE MAIN PANEL
1. Once you've edited your pokemon under the Party Edit, count the number of pokemon in your party.
2. There is a box under all of your party slots called Party Members Amount. Make sure your party member number is the same as the ones that you have above. 1-6. Make shure it is the same number as the pokemon in your party.
ON THE EXPORT ARDS CODE SCREEN
1. After opening, go straight to the Party Pokemon box, under the Main Codes box in the upper left of the window.
2. Check the boxes Pokemon 1 through Pokemon 6, or 1-6 accounting for as many as you have in your party.
3. Here's what people usually forget!, under Pokemon 6 is a more important box, Party Member Amount. IF YOU CHANGED THE NUMBER OF THE POKEMON IN YOUR PARTY AT ALL YOU MUST CHECK THIS..
All that's left over is to export.
In the end:
If you are not editing a save, but sheerly exporting a code for an AR, I recommend this:
1. Make sure your party is empty except for 1 pokemon you are willing to lose. Only 1 in your first slot, no others. Usually for this purpose, you can use a "Dummy Pokemon" AKA a cheap, unwanted pokemon you caught specifically for this code.
(Note: dummy pokemon are commonly used for person-to-person trading in which you and the other person are ether trying to get one pokemon to the other game, or only one person is giving pokemon to the other one-way. In the end, the dummy is released.)
2. Make your party in Pokesav only Empoleon in the first slot. No other pokemon in your party.
3. Mark the Party Members Amount box under it as 1, then Export your code.
4. In the Export ARDS code window, in the Party Pokemon box only check Pokemon 1.
5. Export as usual. Drag the xml into the manager, etc.
If you did as I said, and you only had 1 pokemon in your party when you last saved; the dummy pokemon will be replaced by your Empoleon :3
Tell me if it works or not!