Yes, Vetcove always takes into account your group discounts. All special pricing that your clinic receives and is reflected on a given distributor's website, will also be reflected on Vetcove. The prices you see on Vetcove are your own clinic's final prices, unaltered from what you would see at a supplier's websites.
If you’ve setup an entirely new account number that is associated with GPO pricing, you will want to reconnect your vendor account using your new credentials on the connect supplier page.