A lot of people seem to have difficulty figuring out how mechanical bypass switching works. To help you get a better idea of what is going on I made these diagrams. I hope they help.
First of all mechanical bypass switching is NOT an ON / OFF switch. The bypass switch only routes your signal into or around the FX circuit. It doesn't turn anything ON or OFF.
The first diagram uses a SPDT switch to bypass the signal. Pedals that use this type of bypass switching include the DOD OD-250 and Dunlop Cry Baby wah pedal as well as others. It is NOT true bypass (This is what a lot of manufacturers call "hard wired" bypass). When continuity is between lugs 1 & 2 the signal comes into the switch and goes out thru lug 2 to the output jack. You'll notice that the input signal also goes to the input of the circuit. This is why the circuit can load down your signal and cause tone suckage. When continuity is between lugs 2 & 3 the input comes to the switch and then goes into the circuit's input. The signal then leaves the circuit and enters the switch thru lug 3. And since there is continuity between this lug and lug 2 the processed signal goes on to the output jack.
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This diagram shows how you would go about adding an LED to the above switching arrangement. It requires the use of a DPDT switch in place of the SPDT switch. All you are doing here is adding a second SPDT switch in parallel with the switch in the diagram above. This also is NOT true bypass switching.
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This diagram illustrates how to use a DPDT switch and get true bypass switching. This method does not use an LED unless you want to use the Millenium Bypass circuit with it. I don't particularly care for the MB circuit because it tends to leak and doesn't always turn the LED all the way off.
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This diagram is another example of true bypass switching that uses a DPDT switch. This method however does NOT short the circuit's input to ground. I do NOT recommend using this switching method.
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In order to have true bypass switching AND a status LED you must use a 3PDT switch like this.
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You'll notice that the two diagrams with a diagonal jumper across a pair of the solder lugs also have one lug that is connected to ground (lug 3 of the DPDT stomp switch and lug 2 of the 3PDT stomp switch). This is so when the switch is in Bypass mode the lug connected to the circuit's input gets shorted to ground. This helps to prevent turn ON/OFF pops. If this alone doesn't take care of the pops try adding pull-down resistors to the circuit (1M to 2.2M will work). Pull-down resistors may help but they are primarily for true bypass switching that doesn't short the circuit input to ground as shown in the diagram directly above the 3PDT diagram. If you still have issues with popping make sure the only thing between you and your amp is the pedal in question. This will eliminate any compatibility problems there might be with the rest of your setup. If there is only a popping issue with the pedal when used with the rest of your setup, try powering that pedal with a battery only. This will eliminate the use of a common AC power supply as the cause of the popping. If you still have a popping problem after this you may just have to learn to live with it. Mechanical switching can be prone to problems with the switch's internal contacts bouncing when they make contact with each other. That's just the way it goes sometimes with mechanical switching like this. In cases like these you may have to go with a non-true bypass pedal and live with it's associated tone sucking. In my experience turn ON pops seem to somehow be amp related. I've built several AX84 "High Octane" tube amps and have never had any of my pedals pop. However when I placed my pedals in front of an 18 Watt Lite amp I built they all make popping noises when they were turned ON and OFF. Why this is I don't have a clue.