Stereo would mean you are using two amplifiers at once.
Mono would mean you are using one amplifier only.
If you are using a stereo set-up, your mono pedals would enter your stereo pedals (Pedal A output 1 to Pedal B input 1 at the same time Pedal A output 2 to Pedal B input 2) before entering 2 amps (Pedal B output 1 to amp 1 and output 2 to amp 2).
Some pedals have stereo panning like a short delay between output 1 and 2 to give the wider stereo image. Some pedals have the effected signal on output 1 and DRY on ouput 2.
I believe since you are using output 2 ONLY, you are getting only the dry sound with the pedal engaged. Since you are running a mono set-up, you do not gain anything from using the second stereo output. Hence, refrain from using that and stick to output 1 which is mono for your pedals to function properly.