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You can model the parts individually and then put them into an assembly.
You can create it using a single part file (multibody part) with configurations. One configuration with lid closed, One conguration with lid open. I would only use this method if your lid is intergal to the cover (i.e. a living hinge). Otherwise, use an assembly and create the lid in-context using the features and/or sketches from your cover to match contours.
Take a look at the SW Tutorials, Building Models, Advanced Design and Assembly Mates. They will get you into incontext design and assembly mates.