I’m finding that the AR outputs some muddy low end distortion in the low frequency, this is especially evident when the master distortion and master compressor is used. Any tips on how to reduce this?
I always struggled to get a good internal mix on the AR, somewhat for this reason.
The only way I found to really get over it was to be really careful with anything under about 150hz.
Anything that isn’t a bass or a kick can be hipassed pretty aggressively and resampled if necessary.
Even then I’d still choose between either a subby bass or kick, there’s no room for both once you start pushing the output or the compressor.
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i stick it through audacity and take out the low rumble on their graphic eq works a treat and costs nothing
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I’ve used a Pro-Q4 on the track I’m recording on to cut below 30hz and a small dip at 200hz when recording the main output.
For more tonal control and the ease of fading one track out as fading another track in (and some additional saturation/distortion, send fx and feedback) I’ve started using two mixers.
This has completely remedied that problem. No more mud unless I want it.
In some cases I really like how the compressor and distortion work when there is some excessive low-end energy.
How are you using the two mixers? Are you sending the seperate outputs to the mixer?
Check out the “your setups” thread.
There is a painfully detailed description posted a few days ago. 
lower levels at sources/amp for everything and lower fx levels, especially the reverb
panning stuff that collide
lower compressor threshold
use samples that are cleaner in the lowend