I don't know about get SO to not apply the CC transactions but for the paypal ones the page will show the paypal info but doesn't apply it.
When SO applies the CC transactions, does it actually automatically inform customers via email that their CC payment went through? If it doesn't, then I can just leave it as it is.
when you say "split away", do you mean turn it into a separate order (if say, something wasn't available)? if so, you could delete that other order, no?
Yes, for example, someone orders product A, B, C but product C is sold out. You can select product C and split it away from that order into a new order which you can then delete I believe. Note that if the customer would like to substitute product C with product D, you can't use SO to do it at this stage. Other people suggest to manually make changes in phpmyadmin. However, this can be tedious as you have to change the attributes too...