Professional Services vs. Software Licensing

I run a boutique software business and one challenging area that I am dealing with is how to separate the professional services from the software solution from a monetary perspective. In a nut shell, we have in depth knowledge of the industry we serve and much of our time during the scoping and requirements engagement as well as during the implementation phase of our software solution (Sold at a Fixed Price due to competitive reasons) is educating the client on their workflow as well as other best practices and inevitably we lose money on the implementation and professional management engagement. We typically enter into three (3) year licensing arrangements with the client which eventually softens the implementation and professional services engagement losses. Therefore, I would like some advice in terms of the practicality of separating professional services from the delivery of our software when both the implementation services as well as the professional or consulting services are being performed by the same group of people. Thanks