As for protecting resources, there are some ways to keep most, if not all of them safe from plunders.
The main issue about Warehouses is that they simply don't store enough for them to be worth taking up the construction slot in your town, even with Stockpile 10 researched. However, several high level Warehouses and Stockpile 9 or 10 can save a significant amount of resources. Ideally you would set aside an unimportant supply city and use that as your Warehouse city, so as to not interupt the soldier training in other, larger cities. In this case you would keep a supply of resources sitting aside in this town to protect them in case you fall under attack unawares and don't have time to protect them in other cities, or transport them to safety.
Level 1 can store 10,000 units resource.
|Prerequisite||Required||Quest: Rich Store: Warehouse|
|Costs Time: 10m 00s|
Level 2 can store 30,000 units resource.
|Costs Time: 20m 00s|
Level 3 can store 60,000 units resource.
|Costs Time: 40m 00s|
Level 4 can store 100,000 units resource.
|Costs Time: 1h 20m 00s|
Level 5 can store 150,000 units resource.
|Costs Time: 2h 40m 00s|
Level 6 can store 210,000 units resource.
|Costs Time: 5h 20m 00s|
Level 7 can store 280,000 units resource.
|Costs Time: 10h 40m 00s|
Level 8 can store 360,000 units resource.
|Costs Time: 21h 20m 00s|
Level 9 can store 450,000 units resource.
|Costs Time: 42h 40m 00s|
Level 10 can store 550,000 units resource.
|Costs Time: 83h 20m 00s|