@ Shooting in different levels: As I see in a normal battle a unit always block line of sight. Going into siege and fortress chapter:
"If a player wishes to shoot at fortifications he can ignore the normal targeting rules and may shoot where he wants to
within the normal limitations of range and sight. If you wish to shoot at troops that are on the ramparts of walls or towers then the
normal shooting rules apply and no account is made of damage on the wall or tower itself." (page 91 siege section)
According with the rules you cannot shoot to higher level with your LoS blocked:
"Artillery stands can shoot over any obstacles including friendly stands, that
occupy lower ground than the shooter or target" (page 67 artillery and machines section)
I do not know if there are changes of these rules in other rules versions
@ lilith about the pursuit: I can not imagine exactly the situation. There is a thread in the section of warmaster rules about charge and pursit (quite long but very interesting) that helps me to understand how to make the pursits correctly. Maybe will be interesant for you to read it. Or make a scheme with some image editor to answer you properly.
http://www.sg.tacticalwargames.net/forum/index.php?topic=38.0