How do you store your resources in alliance warehouse?

Find the warehouse on the world map, it should be in your alliance territory, if not ask in your alliance chat where it is.

Tap the building and select the 'Store' option. You can then select how many of your resources you want to send to it. There is a daily transfer limit for what you can send. and a max cap on the total you can store overall. This will go up as you increase your level.

If you want to get resources back then use the 'Remove' option. You can remove as much as you like at any time.