I use a folders to sort through my email so i create several folders by topic. I also use the autoarchive folders so i end up with a lot of empty folders in my inbox.
Can i delete these folders in the inbox or will this impact my archive?
Yes, you can remove those folders without impacting your archive because the items are no longer in the data file you are using.
Unlike a traditional backup in which a copy is made, archived items are moved to a separate Outlook Data File and set aside to be accessed when needed.
Source - How to Archive email in Outlook 2010