Yes this is common situation. Ideally you'd want to have just one place where you manage all of your domains. This is sometimes difficult when you have offer like "Free Domain for Life" while you host with us - in the case of WebHostingHUB.
From the technical stand point it doesn't matter where you keep your domains. I prefer to use Godaddy that gives better offers for domains yearly renewal than $12/year. Especially when you are doing bulk renewal, they give you additional "volume" discounts.
So you can store all you domains at GoDaddy and just keep one with the hosting offer. This way you will be saving the most.