I have done it both ways. Usually, when I've had to change a bad tire on the road, it is connected to the truck. If I have had to do one side or the other while parked, I just loosen the lug nuts on the wheel or wheels on the side needed. Then raise the side needed, and stop when the tires clear the ground. This does no harm to the system. You know, the two front jacks are linked, as are the center and rear on the left and also the same on the right. So, when the trailer is parked, and you raise one side or the other, the fluid moves from one side to the other between the two front jacks, putting no strain on either jack. This is the same thing that happens when you raise or lower the front with all the jacks down, the fluid moves between the two jacks on the left and also the same on the right. The system is set up like there are only three jacks, one in the front and one at the rear on either side, except as they are plumbed with two in each position, you gain the load capacity with smaller jacks doubled up. Hope this makes sense.
Bob & Becky
2012 Chevy 2500HD D/A CC 4WD