Question
In ROW, when specifying a line path, does the positive Y-axis always point to the right, if we assume an observer is standing at the Central Site and is looking towards a terminal? If this is the case, then if I have the GPS coordinates of a path (let’s say the path is 10 km long with 5 km in terminal 1 and 5 km in Terminal 2), all of the GPS Y-coordinates in Terminal 2 will need to be flipped (negated) in order to represent the system accurately. Is this correct? Similarly, even though all conductors have the same relative position in both Terminals 1 and 2, if following the rule as above, do I have to specify two Attribute Sets to take the coordinate system of each terminal into account?

Your considerations are correct. The positive Y-axis always points to the right (or always points to the left, as convenient) if an observer is standing at the Central Site and is looking towards to a terminal. It must be emphasis that this rule has to be applied to define the relative positions (i.e., horizontal separation) of all conductors in a path when defining an Attribute Set.

However, there is a simpler way to deal with this situation: It is not necessary to define the positive Y-axis always pointing to the right assuming that an observer is standing at the Central Site and looking towards a terminal. One can define the Y axis globally, with any direction being positive, as convenient. This decision to be made has nothing to do with the Central Site. The important thing is to describe your right-of-way configuration in ROW with the correct relative positions between conductors, including reflecting the conductors crossing each other (positive or negative conductor Y-coordinates). Obviously, in this way, the Y-coordinates from a GPS don't need to be flipped for a terminal. Moreover, only one Attribute Set needs to be defined if all conductors have the same relative position and conductor characteristics in a path throughout right-of-way system regardless of the number of the terminals. 

The key is to keep consistent! Obviously, the second approach may be more practical and closer to a right-of-way configuration reality.
 
On the other hand, one should keep in mind that, in ROW, the x-coordinate for a path is related to the Central Site. The x-coordinate of a path always starts at the Central Site and increasing towards a terminal.