I'm guessing you're reading an EPUB on eInk as opposed to PDF. The margins used are controlled in the settings (on the LCD side, press Menu, then Settings - eDGe Settings - Reader Preferences - Reader Margin Preferences). Set the margins to "Small" so that the text fill as much of the screen as possible.

For the Journal issues around the margins, recalibrate the eInk screen (on the LCD side, press Menu, then Settings - Sound & Display - Reader Screen Calibrator). Calibration of both the eInk and LCD screens is required from time to time, basically whenever you notice odd response to your stylus/finger.

Finally, the loss of screen space due to the top and bottom menu bars is something we have to live with for now