Having a system in place that allows for customer credit is possible but it is not a supported feature of either the PowerStore or eCart so the implementation would be custom. How it would be implemented would depend on how exactly you wanted the user to use the credit and interact with the site.
If you have things setup so that you manually apply a credit to the user you could have a check of the user record for this credit. Then during checkout allow them to apply it to the order. If they do then you would need to store the credit in a session variable, then create a discount rule that will discount the amount of the session variable.
This is just the start of this type of a setup though and there are some other scenarios you would need to account for. Like the fact that you would not want to send the user to the merchant gateway if the credit were larger than the amount of the purchase.
This is not something that I will be able to give you a detailed step by step guide on but I can try to assist you with any questions that you may have about this or just in general.