On the Motorola Media Link software, you MUST use the Motorola USB cable that came with your phone. Be sure your phone is set to Mass Storage when hooked to the PC.
If it copies the library into two places, it's because of user error (please don't take offense by that, I'm only confident in saying that because I did it before I realized what was going on). In the software there is a Device/Storage Device menu item indicating SD card memory or Internal memory. That setting changes defaults back to Internal whenever MML is updated for some reason. In my case I had set my sync to SD storage, then a week later an dupdate for MML came out and I updated. Next time I connected my phone, it showed no music or playlists in the window to sync, so I thought WTF... Must have lost my arrangement in the update. So I went and checked them off and re-synced, then suddenly got low storage warnings on the device, and noticed two of every playlist on the device.
Had to go in and manually remove all the playlists from the device, then go in and uncheck all the playlists on the Internal storage. You don't have to go through this if you remember to look at the storage setting if you notice something different - I just ham-fisted my way through it the first time it happened to me.
Even worse, is it pays no attention to any Google Music settings.. If you click the setting to download songs from Google Music, and have synced them from your PC and/or phone, it will create double playlists and songs.
All this has been trial by error for me. I have not tried any phone apps for syncing, and use MML to this day with great success now that I understand some of the nuances.
Good luck!