It is 2 steps above a basic link to paypal. Basically on the invoice is a link that contains all the required info to give paypal to build the payment, then once you receive confirmation of the payment, you enter this into the payments section. Really basic and a little manual.
In MyITCRM2, integration with paypal and other gateways will be more locked down, basically the customer will remain on our (myitcrm2's) payments page as the transaction gets handled in the background. Check out http://activemerchant.org/
for details as I think I will integrate this into myitcrm2.
PS: No Credit card details are stored with either application, just for piece of mind. Storing CC details adds layers of security that is required and regulations which is not what we want.