Quote:
database queries will change which are written in c# code.
Actually, it's usually the other way around. You will want to look at your queries and then create indexes based on your queries. So no, your queries will not likely change.
Look at which columns you are using in your WHERE clause and which fields you ORDER BY. Those are good candidates for indexing. But you don't want to just add indexes without there being a reason or need for it.