It matters. The slave engine has to be able to run WOT a bit higher than the master, and run at idle a bit lower than the master. This ensures that the synch can actually make the RPMs exactly the same. It won't hurt anything, but the synch will turn itself off if it can't match RPMs in a minute or two.
Assuming you have the std. Glendining synch, to operate it, you run both engines at about the same speed manually and turn the synch on. After turning the synch on, you push the slave engine throttle all the way up to fast, and when you do, you'll notice the engine does not rev up, it just stays at the same speed as the other (master) engine. Whichever engine is the slave will not respond to your throttle changes once you turn the synch on. Try moving the SB throttle up to max after turning the synch on. Assuming SB is slave, nothing will happen. Now, the master engine's throttle will control both engines speed, keeping them synchronized. It takes some time (less than a minute) for the synch to completely match engine speeds, but when they are really matched, you'll notice the back and forth "thrumming" sound of unsynchronized engines will disappear. Now, when you move the master throttle up or down, the slave will slowly match that speed.
To disengage, move to idle speed and turn the synch off. Now you can pull the slave throttle back to idle and the manual throttle will re-engage, so you now control both engines separately again.
If the synch tries to match engine speeds, but can not bring the slave engine to the same speed (due to engine problems) the synch will turn itself off and the red light goes out. If this happens at high engine speeds, when you pull the master throttle back down, the slave engine will continue at high speed until you re-engage the manual throttle by moving it down. Don't be fooled into thinking it's a runaway engine, it is just left in high speed when the synch disengaged because it couldn't match engines.
Doug