Kevin
It is one of the features of IOS that there are many (MANY) options that you can configure. A principle that I would stress when I was teaching Cisco classes is that just because you COULD do something does not necessarily mean that you SHOULD do something. Cisco provides many of these options to allow you to deal with unusual situations. It does not mean that you should use these options in common situations.
One of the things that you gain as you get more experience with configuring Cisco equipment is better understanding of which configuration options are commonly used and beneficial and which are less commonly used (and should be used with caution).
There might be a situtation where some device is connected to Cisco and the negotiation of duplex does not work as expected (I have seen that, especially on some older gear) and you might want to set the speed for auto negotiation and set the duplex manually. IOS allows you to do this. But I would only do this if I KNEW that I had need of it in a particular situation.
HTH
Rick
HTH
Rick