I used to collect these! They are very colorful, fun, and interesting. They are also expensive and rare in some cases, and being able to protect your cards is always good to learn about. Otherwise, they could get damaged and that could ruin your investments because damage makes cards worth little to no money. Not to mention, after being damaged they may not be playable.
A great way to store your Pokemon cards is to get a binder with card protectors that you can then put your cards into. They can be put in various orders, such as by rarity, type, or any other way you can think of. You can find binders that feature Pokemon characters and you can also get the pages in 100 packs for relatively cheap.
If you want something to store your cards in so that you can still play with them while they are protected from scratches or other damage. They come in a variety of designs so you can get different ones to help you remember which deck is which. You may, for instance, want to use red ones for a fire based deck.
There are also a lot of great tins and boxes that you can buy to store your cards in once they are put into sleeves, or even just loose ones. Some even come loaded with cards, so you can find a set that has a great design and also cards that you're going to want to add to your collection.
1 - http://www.walmart.com/ip/Ultra-Pro-Platinum-Series-Card-Display-Box-9-Pocket-Pages-100-Count/23226168
2 - http://pokevault.com/PokemonCardAccessories/DeckSleeves
3 - http://www.toysrus.com/products/pokemon.jsp