How do you do it? Do you put the metronome on every beat? I'm now also using the drummer of IRealBook as a metronome....
You should use the metronome in different ways. On every beat is good, but it is really important to use it on 2+4, 1+3 , as well as just on 1: especially at faster tempos. When playing in odd meters (3,6,9, etc), it is important to play with the metronome on every beat, every 2 beats, and every three beats. This will get you used to playing in odd meters with a feel for every beat, duple feel or triple feel...A little confusing to write, but take a measure of 6/8 for example: Every beat would be pulses on 1,2,3,4,5,6. Duple: 1,3,5. Triple: 1,4. You can also just set it on one.
Hope that helps.