Hi guys…Newbie here again 
lol. I was wondering…When I get a customer that adds to their order and I want to charge them just the difference on their new total do I just need to use my Auth.Net software to do this or if I submit the updated order through the back-end of the site where I edited the order, will it charge me only the difference or the entire price again. If it is going to charge me the entire amount, is there not a way to just have it charge the difference? I get a LOT of this so I was hoping someone could tell me how to charge only the difference so I don’t have to take the time to put all the address info etc into Auth.Net…that’s so time consuming. Thanks for taking the time to help me out!
Our Payment Capture addon will do this for you (but it assumes you hold cc data on your site). It also supports partial payments and keeps track of what was AUTH versus what's being charged and will conform to Anet's methods of only allowing one CAPTURE against an AUTH.
I'm not sure about your core question about whether cs-cart itself will issue a new AUTH_CAPTURE for the difference or not or whther it will VOID (if caught before the batch) or REFUND the original amount if not. I seriously doubt it is that sophisticated since hwo this is done and rules surrounding it vary from processor to processor. However, if you've previously charged on that transaction, you would have to re-issue the card for any new capture of funds.