Should you use manual or auto focusing, the answer is that it's best to select what suits you. In the main I personally prefer auto focusing as it is much quicker, which is particularly important on those subjects which are more easily disturbed. On some subjects you just cannot afford to take too long setting up your image, if you do you risk losing your opportunity.
Some cameras will have problems auto focusing on smaller subject planes, the Emerald Damselfly being an example. Whilst at rest it spreads its wings and the only realistic focusing point is on the top of its thorax which is a rather small area. In these circumstances manual focusing may be more fruitful.
I only ever have the centre focusing point selected on my camera. This means that when auto focusing you can home in on the centre of the subject and the camera does not focus on other off centre features, for example, the surrounding vegetation.