As soon as you have both EDD and myCRED installed and setup, the myCRED gateway will insert all your point types as a currency in your EDD store. This in turn will allow you to create stores where all prices are in points.
It is important to remember, that if your stores primary currency is points, your users will only be able to checkout using the custom myCRED gateway! All real-currency based gateways will become unusable!
You can find your currency settings on the Downloads > Settings page in your admin area.