There are several ways to protect your resources. What is most effective for you depends on your playing style and how often you play. Also several strategies are written below.
You need to keep your resources safe from being taken away by other players. This if you don't want to be bothered to always have to raid others when you need resources quickly. Your resources that can be raided are Food, Wood, Stone, Metals and Gold. The only one you cannot protect is Gold, it will always get taken away if you're being attacked (depending on the attacker's troops Load). We will discuss below of several ways to protect your resources.
One way to protect your resources is by building a Vault. This building is specifically made for keeping your resources from being raided by others. Build and upgrade it as far as you can to protect more resources. A level 19 Vault protects 950k of each resource except gold and a level 20 protects 1 million of each except gold. If you keep your resources to below that level you won't be losing much if you get attacked.
Advanced players don't need Vault any longer. By raiding castles (or quick farming), they can gather resources pretty easy. And in an old Realm, abandoned cities usually accumulate enough resources in a span of time to be raided. Thus, the need for a Vault is deemed moot. Although, of course, when you get attacked fairly often a Vault can help minimize the loss of resources. Also if you play occasionally or not that often, it is nice to get back into the game with resources ready to use.
If you play more often, an effective way is to train Armored Transports (ATs for short) and send your resources out and recall them at your desired time. This strategy is called Walking. The aim is to send them to another player in your alliance for the length of time you are likely to be away from the game (for example over night or while at work). If your Rapid Deployment research is too high and the time the march takes is too short, you can send a Porter in the march and it will slow it down. Remember, you are looking for a one-way march time because you are recalling the march. If you do forget to recall, the receiving player will eventually have your resources.
Time is important for this strategy, and it is best to memorize some members' distances and march time to quickly transport resources. In case of emergency like being attacked, you can immediately determine which is the best destination to protect your resources.
This Walking strategy for resources and gold can also be used to march the troops to save food consumption. By marching troops to attack any targets, you can save food because no food upkeep for troops that are on march.
This is called Walking the Troops.
As of Christmas Update 2013, every Garrisons of level 18 and up can help in keeping food from being consumed.
If you don't have enough ATs yet to walk all resources you want to save, prioritize on protecting wood and metals first. The reason being, food can be gathered easily from Anthropus Camps (see War 103: Camps Raiding) and many active players should have a large excess of stone and gold due to their long extensive usages (stones mainly for buildings and gold for researches, later for elite troops). Compared to the intensive usages of wood and metals for buildings and trainings, it is best to guard these two resources first.
A pool of resources in one or more members is called Banking. The member that receive all other players' resources ideally still in aBubbled Protection. Making him/ her cannot be attacked and safe from being looted. A free way to do this is by making a new account in different devices, or a fresh new player playing as bank. Members deposit resources and gold to the bank and the bank accepts request for withdrawals. Easy concept. The problems for a bank system are protection time and transports.
A new account have a one week protection bubble, and has the option to extend for another week. That would make the bank vulnerable for attacks after a maximum of two weeks time. Now, building ATs requires a lot of time and resources and two weeks would not be enough unless the player is constantly building and upgrading. In the case of free way banking, the bank usually get razed by members after the protection bubble pops.
Paying banking, which is spending Rubies to always extend the protection bubble can save the trouble of limited time on building ATs and pops-raze. It is an expensive ordeal, and not all alliance have members that are willing to spend. The Water Dragon has a unique skill at Level 20, that prolongs protection bubble.
In an alliance, big-power players have the means to farm more. With large armies, they can raid camps and cities faster than small-power players. And the extra resources unneeded for upgrading and training are left alone, walked or banked. There's another way to protect resources, in a sense of a greater good, that is spreading them to smaller power players. Without any request, you could just send your excess resources to other members and feel good about it.
The downsides of this are marching slots and warp-disabler. Sending to others used one marching slot from the maximum of yourMuster Point can allow. And the receiver cannot warp while having someone sending them something.