I’ve been having some issues with my levels. It seems that my line is peeking, no matter how I have my inputs or outputs set (especially with headphones). Plus my basses always seem MUCH quieter than my guitars. Any and all tips would be greatly appreciated. Thanks!!
Have you tried changing the impedance settings? Does your bass have an active preamp/pickups? That could result in some big differences.
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My basses do have active electronics, yes. I do have a gain boost on the front of my bass presets, since one of my basses it quieter than the others. Where would you recommend the impedance be set at?
My initial thought was that your battery might be running low resulting in less output but regarding impedance, I don’t know if changing the impedance for active vs passive pickups will make much of a difference. Since its easy to experiment, try different impedance value to see if that resolves anything.
I personally have had the best results keeping the big volume knob at 100% for best SNR and tweaking presets/signal chains as needed. I also try to keep everything at unity for I/O but you may need to tweak that as well.
Worst case, always feel free to reach out directly to NDSP support and they will get you sorted! 
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I’m still having issues figuring this out. If anyone could give some additional advice I’d appreciate it!
Sorry it’s still an issue. If nobody adds any input that helps resolve your issue, feel free to reach out to support directly. For official support, please visit support.neuraldsp.com or email support@neuraldsp.com
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I tried setting it up the way you suggested, but it then made the volume knob basically useless. Once I turned it down from max all the volume was gone. It seems frustratingly backwards to need the master volume all the way up, but then have to go into the menu to alter the volume to your liking.