Keep them as two separate batteries. Ok, the negative can be connected permanenty from both batteries. The positives should remain separated.
I don't know what capacity your car alternator has, but an option is to charge your car as per normal and have a high power, 60 Amps or more heatsinked powerdiode in series with the secondary battery charging lead.
Ok, you have to allowe for a 0.7 Volts drop in the diode and heat, hence the heatsink.
You can consider building a voltage sensing circuit which senses that the secondary battery has recovered voltage enough and closing a relay contact in parallel with the series charging diode, for a full top up while the car is still running.
Otherwise tou have to look at fitting a second alternator.
Good luck Raymond