Hi,
I am developing an instructor's manual for the software manufactured by my company. As the manual will include all the modules of the software (and not necessarily what each customer will use) what should I focus on during the analysis phase of this project? Or should I go directly to the design phase?

Any resources that can assist me in preparing customer software training will be greatly appreciated.

Thanks!

You seem to have already done some analysis by finding out that not all customers use all modules. You will also need to find out what features of each module need to be taught. For instance, If there is a feature to import data from floppy disks, maybe that should be left to a job aid and maybe the instructor should focus on getting data from flash drives. (That is an example that may not be specific to your case.) The point is to focus on what is actually needed for the learner to learn, rather than trying to include everything.

Hope - where are you located? There are a number of experienced, extremely knowledgable consultants who would be very happy help you and your company learn what you need to do to approach such a project.