Here is what i do to avoid all the editing and confusing stuff:
1. Go to this site : http://www.pkmdb.com/
2. Look on the right hand side for a box labeled downloads. The pkm are grouped in pkm files(normal run of the mill pokemon ) and event(pokemon distributed via special events, wifi, etc.)
3. Download any you need. Don't need to edit them. when put in your game it will be as if it was traded. If you want them to appear as if you caught them then some edits with pokesav may be required.
Now next step can go two ways depending on what you want:
4a. If you just want to get the pokemon without the pokedex data just use pokesav, open the rom you want to put the pokemon in and load the pokemon you downloaded into either the party or storage boxes.
or if you want the pokedex info also, do this instead of 4a
4b.Go here: http://community.livejournal.com/pokewifi/2167924.html
this shows you a method to pass pkm files from your pc directly to your game via the GTS. In the end the games sees it as if you traded the pokemon even though you don't have to give a pokemon in return. This way when the pokemon goes to your game the pokedex gets updated automatically. One thing to note is that useing this method evolves pokemon that evolve via tradeso if you use this method on for example a haunter it will evolve into a gengar once you receive it.(avoid this by making a minor edit in pokesav and giving it an everstone) .pokemon that evolve via trade while holding an item also evolve if they have tyhe item required when using this method.
