Thats looks really intersting. I will get a look on to it as soon is have this fc. But why do I must hv 2 ds? and my 3ds cant work as "one ds" ?
one DS must be running the "distributed rom" and the other must have an official copy of HG/SS. once the distibuted rom is running on one DS it will send a signal into the air to all DS that are in range (just like gamestop did ffor their special give aways) and if you go to WiFi event or wherever it is you receive wonder card items. you click that and wait it'll say it found "insert pkmn/item name here" then you accept it and it'll transfer said item to your game. then just talk to prof. inside mart/pkmn center to receive them.
pkhex can edit saves like Queno138 said and with pkhex you don't have to go through the trouble of using pkmn bank. as mentioned also by Queno138 it won't recognize any pkmn game on your ds flashcart since dstwo is not a 1:1 game clone if it worked in a way like the sky3ds then it may be possible but it doesnt.
you can use any 3ds/2ds/ds/dsi just need 2 one for hosting and one for your actual game. **only if you choose this method** I have O3DSXL+N3DSXL so wasn't an issue.
if you don't have 2 (systems) then just use pkhex but I can't help with that since I've never used it.
but to my understanding you have to watch how you edit your pkmn. in pkhex or else they can't be transfered to certain games/can't be used in WiFi etc...