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I know it's a basic kind of question, but I genuinely have no idea how this works. Will Pokemon transferred to a Gen 6 game from Black 2 have to go through the Bank before getting to X through Transporter? A step-by-step tutorial would be very helpful.

I've also heard that Pokemon put in the Bank in X can be withdrawn in Y, or a similar scenario can happen. Is it true that I can deposit a Pokemon from one game then withdraw it in another?

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OK I will break it down

One: poke transporter transfers to bank's transport box which can be transferred to a different bank or your box
Two: the transport box must be empty to use poke transporter
Three: Pokemon transported to the next gen are gone forever [more stuff about this below]
four: they can all cross except as stated below [and above] back, oh and transport just transports no crossing
Five: any ilegal Pokemon won't go through.

About the stuff above here is how it works gen 5 -> 6 no going back through transporter gen 6 -> 7 stuck in the future

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This is good to know. But what about trading? Can I put a Pokemon from X in the Bank then withdraw it in Y?
yes you can. It's not really the same as trading, though
It's mostly just so I can trade between my own profiles. I'm currently working on completing the National Pokedex, and I only have one 3DS. Trading with myself is always a real time-saver, especially as I can trade anything I want for a weak Poksmon like Patrat.
Yeah I did that too. You can't evolve Pokemon through bank is what I meant.
That's what the GTS is for.
GTS is good for trading with youreself and like i said they CROSS so they can go between each other for instance x->y s->um and also i don't think it registers to pokedex but you can check for youreself.

Please correct me if i'm wrong :]
The GTS is terrible for trading with yourself. You have to exchange a Pokemon, and, although you can just catch some Route 1 Pokemon, that's still extra time, and, if you're offering some rare or more coveted Pokemon for some Pokemon you can easily get on Route 1, it's not unlikely that anybody who stumbles upon your trade is going to take it. You can also only offer one Pokemon at a time, if my memory is correct, so transferring multiple Pokemon would be very tedious and take a lot of time.