I'm still figuring out the fine points of the game. I really don't know how to take advantage of franchise mode - if someone could post a juicy link it would be much appreciated.
Base running is controlled by the joystick, C Z A and B buttons. To make a runner go an extra base either highlight the runner with the joystick (you'll see orange flashing around him on the splitsceen) and press Z or press C to advance ALL runners - but don't press it twice, or you'll go all the way to third. A and B retreat the runners.
Edit- you can also move a highlighted runner with the D-pad (right-first up-2nd left-third and down-home) This is covered in the instruction manual.
I'm sure you can change lineups and trade players and save, but none of this is covered well in the manual. Just mess around with the options until you figure it out, it shouldn't be too hard.