Well, it might actually help to take several photos, or you could just mark the blank before you cut it to size and drill it.
Mark the center of your pen blank (obviously making a 2-barrel pen), and cross that mark with a line that runs down the lengthwise of the pen ... only an inch or so, right where you're cutting, so that you can line it back up again after the cut.
When you put it on the lathe, the marks should be facing each other, so that the grain pattern lines up.
As you cut the pattern you wish to have on the lathe, on end will naturally become the nib end, and the other will naturally become the finial end... when you pull it off the lathe, keep it properly oriented till you are ready to assemble it. (I like to just keep the parts oriented so that the pen tip and body are always lined up front to back.)
During assembly, make sure your forward section and rear section line up properly where you wish it to be ... for example, do you want the pen to look close to a 1-piece design when the pen is in use, or when the tip is retracted and the pen is not in use?