Comics actually come under the media main category (Books, Magazines), which means they won't qualify for free insertion fees as an auction when you have a store. The listing insertion fee is 5c after the free allocation is used (200 free fixed price / buy it now listings), and you'd be charged the standard $1.50 insertion fee for an auction regardless of how many free listings were still available as part of the standard allocation. 

The FVF goes down from 9.9% to 9.5% for media with a basic store (charged on both item price and postage), but if auctions are a better format for your items, you'd probably be better off without the store as that small break is not going to make up for having to pay $20 per month for the store, plus $1.50 insertion fees (presuming all start prices will be under $100).