Is this going to be printed or is it a personal project that you'll print out and construct at home?
If it's going to be printed is there an existing cutter for this packaging? And if so, can you get hold of the file that outlines the cutter?
Normally, what I'd do, is set up the Illustrator file with all the guides in place including guides for bleed around the various panels, create a cutter in a spot colour on a separate and locked layer.
Then, before designing, I'd save a copy of that file and use the copy to create the artwork for the different-sized panels the right way up so I could clearly see what I was doing. Then when I was happy, I'd either make up a quick mockup to make sure of the orientation of the elements, or if it was simple I'd just group the individual panels, and place and rotate them onto the original document as some of them might need to be upside down.
