It depends on your settings and Android version (a few old versions forced a specific Path). You can set where files are synced in the Device Profile.

I must be crazy spending more time on this.

I'm having a go at syncing to a naked micro-SD card rather than to my Samsung Note 2 phone containing the micro-SD card. Here's what I did...

I removed the micros SD card from my phone and plugged it into my Windows desktop computer. I reformatted it, checked that the MMW file Locations were set to \Music and synced two playlist. All worked well, so I put SD card back in my phone, start MMA and set the location of my music to \Music and all is good. I can see playlist and music as I expect and it plays correctly.

So I then remove the card from the phone, plug it back into the computer, start MMW and check the file locations under Sync Options. Now I see that the root directory has changed to Android\data\com.ventismedia.android.mediamonkey\files.

So the next time I sync I have stuff strewn all over the place, some under \music and some under Android\data\com.ventismedia.android.mediamonkey\files.

What is going on?