Hello,
The short answer, based on your description is yes. You have to copy the entire folder structure to your drive every time.
TEST THE FOLLOWING CAREFULLY:
If you’re building UP a card over time, then it is possible that you could copy the P2 Card to the same place on the Hard drive every time. Files that you had copied last time would simply overwrite themselves. So Premiere Projects that you’ve created based on that media SHOULD remain as they were (that’s your test). Files that you’ve added to the card since the last time you used it would simply be added in.
Alternatively there is a company called imagine products (https://www(dot)imagineproducts(dot)com) that makes some software that allows you to manage P2 media and make clean and independent folder sets. Maybe this is a route you’d prefer.
How do your Premiere Projects work? Are you progressively adding media to the same project over time, or are you making new projects every time you ingest media to the computer (because, say, the subject matter has changed). In either case remember that the location of where you copy the P2 media on to your hard drive can be completely separate from how you organize the Premiere Pro Projects, so you have have multiple projects in various folders on your hard drive importing media from the SAME P2 media folder set that grows over time until you reach the time where you archive it. Make sense?
Hope that points you in a good direction. If I can help more, lemme know…
Alex