Hi, my kitchen sink won't drain and when I turn the disposal on, the sink with the disposal emptys and the right side fills up then I stop the disposal and they both fill up. We have snaked all the visible pipes under the sink. We have also contacted the garbage disposal company (insinkarator) and asked them. We don't know what it is or what step to take next./ Is it possible for there to be a clog in the main pipe and it only effect the sink line?

Sounds like you may have a clog a bit further down the line from your sink. (Just so happens, I have an insinkerator dispaosal in a double sink too) Mine is tied together under the sink, then a single pipe drops down through the floor to the basement to a trap. You might have a clog in a trap somewhere down the line. I'd see if you can access the trap see if your clog is there. Hope this helps.

Rob is on the right track. Remove the trap but be sure you have bucket under it to catch the 2 cups of drain water inside. Rod with a 1/4" rodder that can be turned by hand, there is a 90 elbow about 8" in and it will take some pushing and turning to make it around the corner, rod as far as you can reach. Tell us if things are better or not.

a single pipe that drops down through the floor to the basement to a trap.
Rob, unless that trap is vented you have just described a illegal "S" trap.
The typical sink drainage isn't as Rob describes it.l The typical installation goes into the wall and down a horizontal drain into a vent stack out the roof.
Rasmilittle; Do this, Remove the "J" nbbend from the trap and send your snake into the wall,(see image). As Bob mentioned you'll run into a bead about 8 inches in but once past that you'll only have 6 more feet to put out. After, flush with a tub full of hot water. Good luck, tom

Very right speedball. But I would also mention that even if your trap is vented, it is not allowed to be beneith the floor. Only tubs, showers, floordrains, and floor sinks(mop sinks) can have a trap under floor level. And no s-traps allowed.
The problem definitely is not in the disposal.
Problem is somewhere down line, as Rob stated. What kind of drainage pipes do you have? Pvc, galv, copper?