I was just wondering what was the control strategy used by HOMER when 2 different generators are present in the same system. What is the generator used in priority?

Each hour, HOMER looks at the available dispatchable generators and chooses to operate the one that can produce the required amount of power and operating reserve most cheaply.  The cost per kWh of a generator involves fuel, O&M, and replacement cost.  For details, please refer to section 15.5.3 of our paper "Micropower System Modeling with HOMER". Section15.5.4 explains the economic dispatch logic.

Note that HOMER considers a generator "available" only if there is sufficient fuel for it to operate at full power for one hour.  So if your fuel cell consumes stored hydrogen, that might be a meaningful constraint quite often.

My guess is that your fuel cell has a high O&M cost or a high replacement cost relative to the CHP unit.  If the CHP unit provides heat to serve the thermal load and that reduces the cost of the backup boiler, that gives a further cost advantage to the CHP unit.

One possibility is to use the Schedule tab of the Generator Inputs window to schedule the fuel cell to run all the time or a lot of the time.

Another possibility is to reduce the cost inputs for the fuel cell so that HOMER prefers it to the CHP unit.  For example, you could set the fuel cell's O&M cost to zero.  If you do that, you'll have to manually factor in the O&M cost after the fact to get the costs correct.  A similar alternative is to artificially increase the cost inputs for the CHP unit, then manually subtract the excess cost from the costs that HOMER reports.