Phoneburner now has the ability to set the primary number when dialing from Salesforce.
To set this up, you will want to go to My account/Saleforce integration.
At the bottom of the page you will see the options to choose the phone you want as primary from both the Contacts and Leads views.
See the link below for further info:
If your contacts have more than one number and you don't want to dial the same contact twice, you can adjust your disposition button settings to only dial next contact rather than next number. (see Next Action setting)