You say “rear remote” but that really is ambiguous. I think you mean a rear remote VALVE, but you may mean the rear backhoe connection points.
A valve will apply flow out of either cylinder hose depending on where the lever is placed. As soon as you release the lever the flow to the implement stops (On most valves). There are valves that will hold the flow on but they are not commonly selected for rear remote valves, not unheard of but just not common. If that type of valve is used then the continuous flow path is set and you would need to know which hose out of the valve has continuous flow.
The rear connection points for a back hoe are definitely set up with one being supply and the other being return to the tractor. There again you will need to know which is which to get your hydraulics working correctly for in-feed operation to be correct.
Post a picture of what you are calling “rear remote”.
So the short answer is that the flow to the chipper is probably not directional since the bar can reverse the direction of the roller. And it does not matter which one is connected first or second. And the tractor should probably be not running when you connect the hydraulic lines to make it easier and safer.