1. Save your game in DeSmuMe.
2. Open up PokeGen, and then open up your game save file (.dsv)
3. You should see all your party pokemon and box pokemon on the right.
4. Find the Pokemon you want to evolve, right-click it and click view data.
5. Change the species of the Pokemon into the evolved form.
6. Right-click the Pokemon slot again (the one you previously clicked to view its data) but now click Set.
7. You should see that the slot now shows the evolved form of your Pokemon.
8. Save, then reboot your emulator.
You could also just generate the pokemon from scratch instead of evolving it like that. Open up your save file, create the pokemon you want, then set it into your file.