A run should have the same sort of basic structure as a story:
Setup - Action - Consequence - Reaction - Consequence - Twist/Adversity - Success - Aftershocks.
For a shadowrun, this means:
Setup: The meet for the job, with a Johnson or their fixer.
Planning: Determining how to go about the job; this includes footwork.
Intrusion: Getting In.
The Job: Getting It Done.
Exfiltration: Getting out.
The Meet: Getting paid.
Laying Low: Keep quiet, however you do it.
Depending on the opposition, Complications for a shadowrun can crop up at any time - someone has a plant on the Johnson, and is going to screw with you even before the job offer; the 1e adventure 'DNA/DOA' has this. Someone gets wind of the job while you're doing your footwork, and turns it into a race. You get made on the way in, during the job, or on the way out, and have to pull out the heavy weapons. Or the corp you hit manages to track something (the gizmo, the rumormill, whatever) and jumps everyone during the Meet.
Or, you know, Aztechnology sends goons after you while you're sitting at the bar.
Almost anything, really, is a good idea to look at; the latest idea books (like Jet Set) have things broken down fairly nicely, and there's a whole bunch of them together so you can get a sense of the rhythm of these things.