We get this question more and more into tech support.
The AudioBox series were designed to be a solution for recording musicians, however when these interfaces are used for pro-sumer applications such as web conferencing, there are some unique challenges that you can run into such as this that require some extra steps (and possibly additional hardware) to resolve.
The reason the application only sees one input is because VoIP software is mono audio. The web interface for the VoIP program (ie Skype, GoToMeeting, Google Hangouts, etc) will only take the default mono input which is the Left Channel.
Interestingly, GoToMeeting has it's own PC setup software, yet even though it sees both inputs from the interface, it will only send the left channel to it's web audio interface.
To solve this issue, you'll need to sum your inputs before feeding the audio into the web conference software.
Perhaps others have found ways to do this in software or in hardware. Share your answers here.