Currently, the theme uses paypal as the main payment gateway. However, it is possible to use another but will require code customization.
Question 1: Our company does not want us to use PayPal but rather wants us to work with their existing vendor, Elavon, to process credit cards. Is this possible?
No option on Intuit Quick books integration yet.
Question 2: About half of our clients prefer to be invoiced rather than pay by credit card. Is there any type of integration with Intuit Quick Books?
Again, no feature on this yet. However, this can be implemented through custom coding as the theme is not encrypted and so it can be modified accordingly. For customization jobs, you may contact some of Appthemes certified community partners here
http://www.appthemes.com/partners/.
Question 3:Can we charge for additonal services like addition in our print publication, etc.?