How can I store resources manually?

Resources that are generated are stored automatically in the depots. The only way to protect some of these resources is to be a Farmer class which will give you a set level of protection for each resource depending on your level.

Any resource items (items storage) that you earn through rewards though are safe while you hang on to them. So the safest strategy is to use the generated resources as you earn them and save up any items you earn through rewards to boost your depots only when you need them for an upgrade.