A Ford SD will charge the trailer batteries whenever it is running. When it is not running, the trailer is isolated from the Ford, and cannot run the truck batteries down.
For the OP, yes you can leave your truck running and operate your landing gear and slides, and it will reduce the draw on your trailer batteries. I do that when I will be boondocking and want to conserve as much trailer battery as possible. However, the wiring from your truck is not sufficient to completely supply the current necessary to run landing gear or slide motors, so your trailer battery will still lose some charge, just not as much.
I also agree with the comment that you should be leveled before deploying your slides, which means you will be unhitched. But it does not mean you have to disconnect your shore cord, so you can still run your truck, and that will minimize the draw from the trailer battery. It is good practice, and your landing gear and slide motors will appreciate the additional voltage and current your truck adds. This is just another way to conserve battery power when boondocking, and why not do it?
If you don't use the truck, your generator can provide the added juice, even better actually. But my genny is usually not out of its hole yet at setup time.
I know from personal experience that a GM does not isolate the truck/trailer battery when sitting overnight. They do things a little differently.