Sometimes it takes up to 10 or so minutes for the Aqua mate 2 to begin pumping out anything.
If it is the new Aqua mate 12 (the big blue one, that is like a giant power head) the same thing is true for it.
If it is an earlier model Aquamate, then it is clogged somewhere in the hose, or the fluid control valve is clogged.
The water separator is the thing that spins in the center of the motor where your water basin attaches to it. It looks like a cone shaped fan looking thing. It should be cleaned after every use.
Use your Rainbow separator cleaning brush, or a tooth brush, if you do not have the Rainbow one. They are just like tooth brushes.
Never store your Rainbow canister on your water basin, with or without water in it. It can and will ruin your vacuum in dew time.
You can get manuals either here, http://www.rainbowsystem.com/
or here, http://www.rainvac.com
If you have any more questions let me know. I am a Rainbow seller, and a Rainbow expert also.