I would recommend to listen to episode 87 of the Independent Characters
. I find very interesting/helpful when planning on doing an apoc game.
If you are planning on hosting it at a store I would
A) Check when is a good time/date
B1) have a limited number of people able to attend
B2) Restrict the amount of points/superheavies/lords of war/etc that each player can bring.
C) preferably have the teams be predetermined
D) Balance the teams by how powerful the army/player is - don't put all the armies that have superheavies/death galore all on one side, even if it is fluffy where it would be all imperial vs chaos - no one likes getting their ass handed to them for 8+ hours
E) BREAKS, plan accordingly and efficiently
F) I highly recommend timed rounds - you have 15-30 minutes per phase so if you didn't move/shoot/assault with something then that sucks. (at least with the movement portions of the phases - if the assault just needs dice to be rolled let them roll dice.
G) don't sweat the small stuffs - who gives a shit where the people that died from were pulled from - this is a fun game, not a competition.
FOOD! - it's important yo - make sure people either bring money for pizza or potluck it.
As for the actual mission ideas - I would just use one from the apoc book - or a battle mission/alter of war.