Arduino read PWM and control motors by RS485 and a special protocol


I am creating an autonomous boat and I need some help for arduino programming.

I have a Pixhawk autopilot and I want to read the PWM output of the throttle to control two motors.

I use PulseIn command and I think it's not working so bad... If you have others ideas to read the PWM output I am open !

My problem it's to control the motors. I have two motors controled by a special protocol based on RS485 communication.

So I want to read my PWM signal input and transform her into the good protocol to control the both isolated motors !

To create the protocol I think it's not so complicated... I can find informations on internet but you can advice me if you have ideas.

I have problem to make the RS485... If I send RX and TX on a TTL to RS485 converter shield, I can't control my two motors in parrallel... 

And the both motors have to be isolated !

Have you ideas of how I can isolate and convert the output of the arduino or if I have to separate my communication in two different RX and TX ?

Or maybe the Pixhawk can have options to control the throttle like this... I don't know...

If you see others problematics points you can advice me...

Thank you so much for your help and for your time !

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