One composite design of several tricks I use is basically as below (although finessed more, a longer range and varying according to local geography and geology).
v target zone v (usually longer)
#
# H<-- X
# ################\ ___DEPOT__ X
# #################### ###### ##X
# ###############################X
# X
#################################X
#################################X
The target zone is entered from the side (into/out of the screen), sometimes the target zone is an actual "tongue" of rock, with the sides also channelled down towards the lower area (stone gathering level), but which can be additionally protected by lowerable bridges if I don't fancy the flyable gaps.
The siege engine(s, usually three, staggered) sit on the same level as the target zone floor, the depot is below. By the time enemies are within 'scare' range of the siege engine, they're not shootable, and I might well have raised the bridges (one from the depot to the outside world, one from the inner fort to the depot)
I can have any siege operators (I must admit I've not used them much, recently, but when I do it's almost exclusively catapults, despite the 'glyphs' I drew the siege engine in) practice constantly, the stones they use hit the end and are available for further use by siege operators or other stone-users. I can pause them when attack is obvious, if I want instant response, but it gives them a chance to get their reload speeds up through loads of practice.
Alternately:
######
##################___## <- 'practice' hole, for when facing north
...........v HS^S##
...........v H<+-X# <- Siege engine, set either to north or west through fortifications
...........v HS|S##
#################H#####
^^^^^^^^^^^ ^^^^^
kill-zone & sunken approach
(Seconded on the catapults through fortifications, BTW.)
I've also done the following:
Raisable bridge
|
v
#############################
__ H<--X
###############\ # ####X
###################### #####X
#side view############ X
############################X
Top view
############################
++++++++++++++++v =+ HSSS
++entryway++++++v =+ H<--
++++++++++++++++v =+ HSSS
#############+++############
#+++++#
(usually #+++++#
depot has #DEPOT#
bridges #+++++#
and moats #+++++#
for both ###+###
inwards and outwards access,
as well, but this is simplified)
Bridge up for training (also protection from ranged enemies who might turn up and look dangerous), bridge down for sending all shots straight down the corridor at enemies.
Staggering the siege engines might go as follows:
#############
####SSS######
H<--SSS###
HSSS<--SSS
H...SSS<--
##########SSS
#############
In response to the the largely ninjaing post from tolkafox, about staggering, channels in front of fortifications, etc, you can always train your SOps on catapults, with spare (or recoverable) stone, even if you're going to be using a ballista or three in your main defence in which you can't engineer a reliable ammo-recovery system. Same skill, and all.
(But for a ballista version of the staggered defence, watch out for that 1x3 space to the side of the forward engine, with the rear engine shoots through it. Better put a restricted zone. Also directly in front of the middle one, possibly, just in case the forward gunner decides to wander through those tiles to man his own weapon.)