It sounds like you're working as an employee - if so, I would ask your employer how they'd like you to manage files as it's likely they have a process already established. It really helps if everyone uses the same system because it's then easier to pick up another person's work and run with it if they're sick etc.
If you're the only one working in your area then yes, you have control over what the process should be!
In general you will find it useful to have a folder per project that stores your artwork (I like to keep drafts and separate them by number), linked files (such as images & spreadsheets) any files you were supplied by other team members and any reference or inspirational pieces. How big the job is determines if you organise all of these files within folders; I do find it to be a good discipline to maintain even in the smallest jobs though. Predictability is a fabulous thing then it comes to filing! Because everything is stored in one place I don't bother to package my files before archiving.
Every studio has a different job numbering system. I've worked places which use a database to record job details and generate a unique ID, and others which have a rule to base the ID off. In my own freelance work I choose the first three letters of the client and then number each of their jobs sequentially.
Common files, such as your company logo and any collaborators/suppliers are often useful stored on a common server instead of within your job folder as this reduces the chance of multiple variations.
I don't have as much experience setting up back up systems so I can't be as useful to you there sorry!
You have been brilliant and very helpful. Thank you for taking the time to respond. I am in the process of making folders and placing all relevant files in the directory. I have named them via magazine and date.
I did a package and then compressed the older work but left a small compression PDF file on the outside so I know which project it was.
ID Numbers would be great to keep the job number in line with the project.