If you use Pokebank, do you get the payment option at the end of your year or do you have to pay to download it? Also, what happens to Pokemon left in it after you stop paying?
There is a message saying 'Your Pass has Expired' (Or something like that)
Your Pokemon will be gone after your Pass expires. You have a period of time to get out the Pokemon quickly though.
If your trial pass or annual pass expires and you do not purchase a new pass, you can still withdraw your Pokémon from Pokémon Bank for a set period of time. However, once that set period of time ends, any Pokémon remaining in your Pokémon Bank Boxes will be lost. Be sure to withdraw your deposited Pokémon as soon as possible, or purchase a new annual pass.
Source
You Pay before you download. After your time period is up you have a short amount of time to either pay again, or remove your Pokemon from the bank. After this amount of time all Pokemon left in the bank will be Deleted.
Source: Expierience and http://www.pokemonbank.com/en-us/faq/