How to measure accurately utilisation and commercialisation of our engineering resource and control them

We apply Agile into our process but reallize that we are not operating and control our project billable and non-billable ( R&D) effectively. Therefore, we are looking for how to calculate accurately utilisation and commercialisation of our engineering resource. We want to optimize our productivity and financial effectiveness. What we need to do are creating time tracking mechanisms and processes, capacity monitoring and planning, calculating our investment and feed that into our commercialisation of whatever products we produce, defining our resource processes, management and utilisation against our commercial objectives. We want to focus on R&D project to compete in the market and get more money. However, we are all tech guys and do not know what to do exactly. We would be really appriaciate it If anyone could help and explain.