Logic is important for all areas of life. However, when it comes to debate, logic holds a very important place. In fact, argumentation theory is the study of how sound conclusions can be reached through reasoning, based on sound premises.
In light of this, the advantage of studying logic is clear. If your arguments are logical, then you will be able to reach a conclusion that is not only true, but also cogent enough for you to win your debate.
So, if you are discussing prayer in school, then you should first seek to establish your premise. If you premise is that there should be a separation between church and state, then prayer should not be in school. However, if you premise is that there should be freedom of religion, then people should have the option to pray in school, if they want it. What you want to be is consistent, based on your premise.