1. Is there way to ad trans ID. from Authorizenet To the invoice?
Currently the cart emails the order id generated by the cart in the email confirmations and does not email the transaction id from authorize.net. We would have to add a new token for the email confirmations in order to support this requirement.
2. Can we switch the ship and billing one the invoice so that billing on the left and not the right?
Which invoice are you referring to the email confirmation or the invoice created in the manage orders from the store admin menu?
3. How does a customer that has recurring bill update their C.C. Data ?
Right now in the cart their is no way for the customer to update their credit card for recurring billing if their credit card has declined or if they want to use a different credit card. You will have to get the new credit card from the customer over the phone then login to the authorize.net virtual terminal and update the customer Automated Recurring Billing (ARB) record with the new credit card info.