Click Compression Options -> External Compression -> Use external program for compression. In the drop-down menu, set the Parameter passing scheme to "User Defined Encoder", and the File Extension to ".mpc". Then point to the location of mppenc.exe and copy&paste the following line into the field labeled Additional command line options (modify the quality setting and add or remove fields to your preference):
"--standard --ape2 --artist "%a" --title "%t" --album "%g" --year "%y" --track "%n" --genre "%m" --comment "BlaBla" %s".
Disable Add ID3 tag so that all files will now be tagged using the recommended APEv2-Tags.
You should have a look at Case's EAC guide.
Musepack is a purely variable bitrate format and does not work at a constant bitrate. A big part of Musepack's quality comes from its highly variable bitrate handling which results in low bitrate for less demanding regions of the audio data and higher bitrate where it's needed. This allows MPC files to be as small as possible and not lose any valuable bits like encoders that work at a constant bitrate. After all, the purpose of a lossy audio encoder is to provide the highest possible quality at the lowest possible file size, and Musepack represents progress, as opposed to old, suboptimal legacy methods.
You should not use any additional commands (like --ltq fil , --ms 0) to "tune" quality, except for the Quality-Switch (--quality 5.5 , --quality 7.2 , ...). Just use the Quality-Switch for any kind of fine-tuning as it gives the most optimized quality possible.
The XLevel-Switch is used to avoid internal clipping as well as possible. Starting from version 1.15s, "--xlevel" is no longer needed as it's used by default. Instead, there is a "--noxlevel" switch.