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Pedal noob.

After having my setup for about 9 months now, I find that I am still learning how everything works.

There are some songs that I play that I adjust the amp EQ so that the treble and high mids are turned about all of the way down. I did not realize that this was having a reaction on certain pedals. Without the treble I wasn’t getting any effect.

I moved the pedals outside of my effects loop and they function fine, after my Hyper Luminal.

After much confusion and trouble shooting I’ve come to think that I have possibly two options.
1. Continue to adjust the EQ on the amp for the tone for which I am trying to achieve and Get a clean boost.
2. Leave the EQ on the amp alone for signal strength and EQ the signal after the effects.

Thoughts?
 
Effects loop is only for things that you specifically want or need to be after your amp's preamp. Most pedals go in front of the amp input, but stuff like chorus and delay can be perfectly fine in the loop. As you may have found, though, take away some of what the effects are "feeding" on and you lose a lot of the effect. Like a phaser won't have much to do without some mids and treble, for instance.

If you have some songs that are all lows, like a dubby reggae tone maybe, have you tried just killing the tone knob on the bass first? that usually gets me enough rolloff to do that sort of sound.

If not, though, just try your whole pedal chain in front of the amp instead, only moving things to the loop if you need them to pick up the preamp's flavor before them.

Good luck!!