I usually think of the Runs that I design in terms of "Scenes". There's a Beginning "Scene" and usually an Ending Climax "Scene", with a mix in between. Sometimes the players may not even run into certain scenes I've written. Sometimes this is intentional. The Runners might end up doing either Scene B or Scene C, depending on a choice they made in Scene A.
Sometimes my players come up with ideas that I haven't thought of, and I have to improvise a Scene on the fly, or they'll skip over a Scene entirely.
For example, legwork on their target might indicate some valuable information to be had at Dante's Inferno. I'll write up a scene for Dante's, and devise a couple different ways the players could get the information they're looking for. However, my players could (and often do) simply disregard the lead they got pointing them to Dante's, and go off in search of that information elsewhere instead.
Sometimes in my head I come up with a great idea for a Scene completely separate from the Campaign. I'll go over the campaign and sort of think about how I could work this Scene into the plot. I'm actually in the middle of one of those now. I've got my campaign mostly written, but came up with an idea for a great Scene to use. I'm working it in as sort of a "Secondary Objective" for the Runners to complete while they're on their Run. I haven't quite determined where in the campaign I'm going to stick the plot hook for this "Secondary Objective" yet though. My Runners tend to do their runs on the straight and narrow... do the job, get back to Mr. Johnson, get paid. I have to come up with a good way to distract them.