Reducing noise is all about finding the right balance between the controls, not only on the Fly Rig (or any pedal) but also with the controls of the other gear/amps with which it's being used. Here's some helpful info and suggestions:
With any and all pedals, it's generally a good idea to start with most knobs at 12:00, which is typically fairly neutral.
As it relates to the settings of active vs. passive controls, know that positions are not created equal. At 12:00, active EQ controls would be the equivalent to maximum on a conventional passive tone control. It’s possible that 12:00 might actually be a bit high, as you'd rarely find anyone setting their amp's treble knob on max. It wouldn't hurt to bring Bass, Mid and Treble, all down to 10:00, which is more like an "8" on a passive tone control.
With Level and Drive, we recommend starting at minimum. Bring up Level until you can hear well enough. At that point, increase Drive little by little --while you’re playing-- to see how far you can go before crossing the line between clean and dirty. Since Drive begins its travel as an input sensitivity control (to ensure you're getting a good strong signal from your instrument into the pedal's circuitry), it may remain clean for a while, then eventually reach the threshold of overdrive, depending on the output of your pickups. With a humbucker, that might be 10:00 and with a single-coil, it might be 12:00. It varies from instrument to instrument, so you have to experiment to find it.
Keep in mind the interactive nature of the controls. Active EQ controls, for example, affect the volume because they cut and boost the dB level of specific frequencies. And if it's not already obvious, using overdrive/distortion will often add hiss. So the more Drive you dial up, the more you may need to cut the Treble.
Lastly, there’s "unity gain." This is a fancy term meaning having the same volume coming from your amp, whether the effect is on or off. Even if you will ultimately be running straight to the PA, it's good to find the unity gain position of the Level knob by running into an amp, and turning the pedal on and off while adjusting the Level control. You certainly don’t want a drop in volume when the pedal's engaged, nor do you want a massive increase in volume that might overload the input of the next device, causing a harsh, un-musical break-up.