If you want to see actual examples of the how and why, download a copy of the Futaba 8U Super radio manual.

http://www.futaba-rc.com/manuals/index.html

When not using a Y cord, you use what is called mixing.
A lot of the mixes are pre canned in the radio, such as the dual elevator. One reason this is used is for planes with 2 ele servos in the tail. The servos are actually mounted in the opposite sides of the fuse. If you could only use a Y cord, the servos would rotate in opposite directions. Using the mix in the TX allows the servos to operate together off of 2 different channels and rotate the same direction. (as if there was an axle connecting them)

There are also free mixes available in the computer radios. With these, it is pretty much up to your imagination. Over the summer, I put floats on my Kadet. Instead of fooling with mech linkage from the rudder to the water rudder, I added a servo for the water rudder and used a mix to slave it to the rudder channel.