Lots of good advice above. I'd add a second to Brian's comment about staying with smaller flies (12-16) early in the season, maybe a bit bigger later.
I usually fish two chiro's at a time, but honestly I'd say probably 90% of fish are on the lower fly.
Also, the "dangling" technique Brian mentions above is very useful when the water is roily - too much ripple or waves, and chiro's under an indicator are not overly effective (too much movement of the indicator, bobbing the flies - most natural chironomids don't move this much). So "dangling", where you compensate a bit for your boat movement in the waves to minimize chiro movement can be very useful on windy days in particular.
Don't be afraid to try odd colors - my best chiro patterns have consistently been in UV purples and pinks (probably more of an attractor pattern than actual imitation).