How to Choose Attacks
It is easy to see how certain Pokemon become more efficient with certain maps. This is why you cannot just choose six Pokemon and forget about the rest. It is important to invest the time and energy to level up as many different types of Pokemon. Also, it is important to know that a Pokemon's type does not limit it's attack variants. A fire Pokemon for example, is not necessarily limited to fire based attacks (though it would certainly have those, but it may also have poison attacks and other elements as well). Knowing the various traits of your attack abilities and being able to change to the most appropriate type is the key to winning many battles.
In most cases, you will want to replay a stage after having played through the waves and checking out the different Pokemon that appear. There are plenty of times when you will suddenly be faced with a strange new Pokemon that appear to be able to withstand most of the damage that your towers will deal. In fact, it is not rare to encounter a few that are practically impervious to most damage (steel Pokemon types are resistant to at least five different attacks). At this point, it is important to know what kind it is and what it is weak against - and you should keep note of that for all the various types of creatures that will appear in the waves. Then once you have the info, you can replay the stage again and this time, bring the right kind of Pokemon for combat.
Once you know what attack to use, click on the Pokemon whose attack you want to change. A new screen will pop up and allow you to choose among its different attacks on what it should use. For the most part, stick to using base damage as a reference for effectiveness. The second thing to look out for is the element being used - make sure that it will deal normal or double the expected damage. Some of you may be thinking that it would be a great idea to overwrite any defensive type skill such as "harden" with offensive attacks. This is only true if you are planning to keep those Pokemon strictly for attacking roles. The game will later turn the table on you and will be required to attack, which means any ability to keep your health up will suddenly become really crucial to have.