Add Order api

So I wanted to use add order to price override for shipping, can I use this from a hook then have payment proceed as usual or do I need to cancel the default action somehow and how do I do that. Say in OnBeforeCheckout

function inject_beforecheckout($vars){
global $smarty;
pull smarty variables from checkout page total price, my shipping variable add them together to get my real total.
//Create client with details from smarty variables
call addorder from internal api.
//call capture payment here? or is it necessary?
//Generate my own invoice here?
//Prevent default action... Somehow.
}

Basically I just want to avoid charging the customer twice for a custom product.
I'll run some test cases now and see what I come up with. Otherwise I'd be willing to pay the creator a modest sum to give me some help with it. Or anybody that can do this in a way that three requirements are met.

Shipping shows on the invoice and
The customer pays only once.
Tax works as usual.