With effect of build from Aug 2016 onwards, Audio FX will NOT be replaced by any third-party equalizer.
The ONLY solution is to first remove Audio FX by using Root Uninstaller then flash DSP Manager.
DSP Manager is an Equalizer that was once as default equalizer since CM7 and it performs almost identical to beats audio. (Best features: Dynamic Compression & Bass Boost)
Since CyanogenMod has stopped / abandoned work for DSP Manager on CM12 onwards,
I have a solution and had 2 zip files tested and FULLY working on CM12.1 & CM13 (should be also fully compatible with any versions of AOSP, modded, stock Lollipop and future Roms)
I have attached 2 zips (eng.stk's modded zip + patch) that will be needed in order to get the sound enhancement working.
1. Flash the modded v5.0.8 zip
2. Flash the patch(DSP.zip)
If it does not work after performing 2 flashes as mentioned, try flashing v5.0.8 zip on top again after flashing the original DSP zip.
(No wipes required)
Big shout out to CyanogenMod Team and @eng.stk
Be sure to check out @eng.stk other modded equalizer works.
Original music player(Apollo) has also been included.