1) Yes, you would need to delete the cart display code from the cart.php page, and remove the eCart Continue Shopping, eCart Update Cart and eCart Checkout server behaviors, then reapply the cart display manager to the page.
2) see the "Changing PowerStore's Payment Gateway with eCart" Tutorial in the how to section of the eCart support page:
powerstore/
3) You can have flat shipping rates on top of the UPS or FedEx rates if you like.