If you're just expressing your opinion in a normal sentence, you say:

I prefer bottled water.

I make a good living as a waiter.

You say "I do (do something)" when you're contrasting the things you do with the things that you don't do. So, for example, if someone said that you shouldn't use bottled water, this sentence:

I do prefer bottled water.

...is a contrast to what that person said. 

Likewise, this sentence:

I do make a good living as a waiter.

...can be used if someone says that waiters don't make a lot of money.