I guess the word 'properly' depends on the type of work you are doing already...are you flying solo, or do you have any resource/person at your shop to train you?.
You could be using the system one of a hundred ways.....
Are you using the ROOM or NORM workflow?
Are you using EPS FPO's, PDF FPO's, or nothing at all?
What do you use for imposition? (Preps?) ---JDF or EPS?
Do you rip EPS or PDF? Do you use the PDF Trap Engine?
The basic thing here is to determine what profiles are setup that your company uses....look at the setting for these profiles and look up the info in the manual.
Look for a 'guide' of how a typical job progresses through your workflow.
i.e. - my shop (v13)
current 'typical' workflow. (we use JDF imposition at this point, as opposed to the EPS/FPO imposition method)
-Register PDFs or single page EPS to Prescan, Trap, Rip, FPO, and Monitor Proof profiles.
-Register JDF of imposition and allow it to place pages from the previous step.
-Produce Proofs, Create InkZone (CIP3/4 Data), Plot