I am configuring a small motor boat (40HP outboard). I chose an AGM starter battery for engine and windlass. The house battery is a LiFePO4, for all the rest (fridge, coffee maker, GPS, lights, etc.). My proposed setup is depicted in the diagram below. The Cyrix should enable charging the AGM first, then the Lithium. To adjust the voltage, I’ve inserted a DC/DC so the lithium battery gets the recommended voltage. In case I need and emergency start, I will parallel the two batteries manually instead of using the Cyrix parallel. Is this setup advisable?
If you have a DC to DC charger then you do not need the Cyrix, the DC to DC charger can be set to only come on when the AGM batteries are charging.
Secondly, many LiFePO4 batteries have BMS current output limits, you need to check if it is OK to parallel the house battery for engine starting. If your start current is too high the BMS will just shut down.
Thanks for your feedback. My DC/DC charger is not smart, as soon as it gets at least 8V it kicks in. I’m afraid it would drain the starter battery in favor of the lithium. My real concern is the alternator overheating.
Now understand the Cyrix, makes sense. Usually if the DC to DC capacity is half the alternator capacity it should be OK.
Looks good to me. Good Idea with the Cyrix Relais.
I had a similar setup few years ago in my camper van and it worked very well.
The solution with the emergency parallel switch is mandatory, there will be these one particular day where you need it! 
But I would add some pre-charge circuit, kind of a soft-start, for the parallel switch,to first match the batterie voltages and to avoind high inrush currents because of very different battery voltages.
You could just use some push button and a 12V 10W bulb in parallel to the parallel switch to first “align” the voltages and the you connect both parallel to start the motor.