And I would have thought that marking them up as bold, italic or both would just help to mark them out as the transitoins from one section to another. That's if you're talking about using them as headings. If you're referring to dates within the text (i.e. the journal entry refers to other dates - "As on 3rd August, I found myself faced with a dilemma") just treat them as part of the text.

I'm not sure what the term for a short story in journal form is - I assume there is one (as per epistolary). I would think that you'd start each entry as a new "chapter" - if you had the space and your typesetters were amenable, each entry should start a new page.