Assuming you have two trucks per rail, mount a plate FIRMLY on the "master" rail/truck set, and have the plate overlap and rest upon the two far-side trucks. SHCS the plate only loosely on the far side, so that the plate will drag the slave-rail trucks as it moves. Mount the indicator (0.0005" or better) on the far/slave side of the plate, so that the probe is contacting the rail close to the base. Rails usually have a master edge, denoted by a ground line, measure that edge if you can.
Secure the master rail firmly against a milled or other precision ledge or edge. Basically, get the master rail straight. In longer lengths, they WON'T be straight, you must make it so when you install it. Secure the slave rail using SHCS and lock washers only tight enough so they will move with some gentle taps of a rubber mallet, or some type of screw arrangement which bears on the rail. Move the plate by hand and note the indicator reading at various points. Work from the center outwards. First, secure the slave rail center bolt relatively firmly. Note the reading. Move to the next bolt hole, make it read the same as the center, secure that one. Reverse direction, go to the next unsecured hole location. Repeat the tightening process from the center outwards. A long rail can easily have significant arc. This procedure should take care of it and create a parallel rail system.