don't forget that Shadowrun is a 3 worlds World, if you design your own game
you have to think about the Astral, The Matrix (and Drones) and the "Physical" World.
Normally I Start with the Host (because it's the most easy with the new Matrix rules). Found out it's rating, now it's Stats and IC/deckers and after that his metaphore (I recently design a DocWagon Host. it's valley with patients link to the trees, when it's raining it mean that an emergency is happening, etc.)
Now think of how you see your site, does it use drones ? Grunts ? Critters (I like that one) ? Does it Have patrol ? What type of weapon do your gards have ? find a kwirk (he is pist off when is coworker put milk in is coffee) for one of the guard and bingo.
after that Magical Security : How Many Spirits ? wich rating ? for what purpose they are there (In my DocWagon clinic the Air Spirit protecting the Helipad have light that show if the building need to be quarantine for ariel vector pathogen and he have a protocol if this light is on) ? Do you have Mana Barrier ? wich rating ? for what ? and what Happen if one of the above is dispel ? (DocWagon : if my mana wall/spirit is dispel a mage and a patrol are dispatch to asses the situation) ? Finally, how this security influence your physical one ?
don't forget to put some fluf in it, junk data that are useles to the run but could be cool, funny, gross, totally useless
and don't follow the rules. Players know (normally) the rules their character will be using, trust them. If they don't know, you don't know, don't find it in the book : Make one ! You know the logic behind the game, you could do it.
Trust yourself, you're way better than you think