Although the software is available on the official website of the developer, there is no troubleshooting information about settings and configuration provided to public use. You have to take advantage of the Customer Support in order to get an answer to this question. On the other hand, I don't think there is a possibility to use the chambers independently. The information gathered from the images suggest that one chamber can be used as a time. After all the processes are finished for that chamber, you move to the next one.
Contact Support: http://www.med-associates.com/customer-portal/