Yes and often times how they look will be out of your hands. You publish in magazine and their editor+designer will change your underlines to italic and your italics to bold because thats how it makes sense in their publication.

Of course you are both writer and publisher you are also in control of the design. But when you are writing you shouldn't be thinking about how to present the text. These are almost always different processes (except rarer things like poetry or experimental prose that rely on whitespace). Write > edit > present/design.