The plan is to have the Sony/Borders eBook Store work independently AND integrated with the new Borders.com coming in February.
Steps are currently underway to begin testing in-store downloads for eBooks at select locations.
Presently, they already have services in place to allow downloads of music in-store, with downloads of audiobooks coming in January.
http://www.bordersmedia.com/godigital/
With in-store capability, this should allow the ebook downloads to qualify for select discounts through the Borders Rewards membership program.