Combining fleets togehter impossible?

[Tellos Athenaios]

If one of the admirals has a better quality ship he'll refuse to give up command to the other.
If one of the admirals has is a better general he'll refuse to give up command to the other.

So if your pentekonteroi one is the best, the only solution on this level is to let him depart for one of your docks and let him sit in the dock whilst a trireme is trained at the same location. Then he'll be using a trireme for flagship which allows him to merge with other, lesser trireme-admirals.

All the other ships can be simply separated from the pentekonteroi flagship and merged with the other fleets.

EDIT: Not to mention what beatoangelico mentioned....