I'm currently having trouble getting my custom music to play, but it worked for someone else so...
- Convert your MP3s to WAV format and create a folder named "Music" in Skyrim's Data folder. Put your WAVs in there or in any subfolders.
Open up the CK and go to Audio > Music Tracks. Right click any entry and click "New". Enter a name in the ID field and select "Single Track" from the dropdown list. Now click "Choose File" and you'll be in the Music folder you just created. Select the desired WAV. If your music will play in battles, make sure you also choose a file that plays when combat ends, and choose some points in the combat music for it to play (in [minute]:[second] format). There should already be some files for finishing music, but you might want to add some that fits your track. I'm not sure what happens if you don't do this. Also, if you want just your custom made locations to have the music, you can click the "Has Conditions" checkbox and set conditions on the Conditions tab.
Go to Audio > Audio Types, right-click the category you want to add the new music to, and click Edit. Right click the list of tracks the audio type is using, click Add, and find the track you just added. Save the mod and make sure it's activated.
As I said before, I'm still trying to get my custom music to work. I used Switch Sound File Converter to convert my MP3s, so if you use something else and it works for you, then by all means report back.