Alright, this sounds pretty good. So when the user registers you will want to either record the payment choice or assign one for the user.
For the checkout itself you would start with the regular linkpoint checkout. Once you have both of these in place and working the next step would be to get the credit scenario working.
For this you would start out by either querying your user's table to see what type of payment method they will use, or you can store that columns info in a session variable when the user logs in.
You would use this value for the payment method on the checkout page, if the user is paying with the credit account then you would not show the regular billing form but an alternative form to gather the info you need. This alternative form can post to either the same confirm page or an alternate one. If you use the same confirm page you will need to do some customizing of it to get it working with the credit account.
If you use another confirm page it may be easier to setup. When paying with the credit account you would need to query the account info to see what type of credit they have. If they have enough available then you can let them confirm the transaction and subtract the total from the available credit. If there is not enough available credit you can inform them of this and allow them to go back to the cart to update it.
This is a high level overview of how you could have this setup. When it comes to the credit account part please post back with a little more detail about how this part should work and I will advise you on what I can.