As far as I know, things like fonts and font sizes are decided by the publisher. When it's just the basic manuscript, I usually use italics to indicate something looks different, e.g. when my characters are texting. (In YA in particular, that sometimes gets turned into a graphic that looks like actual text bubbles, or it'll get formatted differently.)
But like MKWrites_318 said, at the querying stage it's mostly about readability, so I wouldn't recommend playing around with fonts and font sizes. That's something that can be brought up once the book has sold.