Are you using Gateway/Emunand for your themes or using CFW?
GATEWAY METHOD
If its Gateway your using. Just put both files (bgm.bcstm/body_LZ) on the route of your sd-card, boot up emunand then trigger a proper Nintendo theme first, not a default theme, then boot into your Home Extdatatool.cia icon/banner icon, (if you have not installed it yet, install your Home Extdata.cia file with the DevMenu make sure you have that file as well on the route of your sd-card at the same time as the others), then in the Home extdata screen click on the top one first, Copy extdata SaveData.dat to sd, then next click on Enable Theme-cache and last click on Copy Theme cache from sd to extdata and then just reboot your 3DS the theme and the music should both work in emunand soon as you boot back into it.
HOMEBREW METHOD
If your using the other way, Homebrew just put the whole 3DS folder into the route of your sd card put both theme files into your Home Extdata folder and boot Home extdata from Homebrew on your 3DS and repeat the same steps as above.