The Toilet has no water in it after being flushed. Also when the toilet upstairs is flushed, the main floor toilet (the one with no water in it) makes a funny noise. The plumber said to pour water down this tube sticking up on the roof to unclog it but I'm just not sure. He won't do it as it is "not something a plumber does" Any ideas for fixing the problem?

Get another plumber. Take the top off the toilet tank. Reattach the little refill tube from the fill valve to the overflow pipe.

HkStraoud said it: reconnect fill tube inside toilet tank. It probably slipped free from the overflow tube.