Replacing Stage Music Headers

First step is to find a nus3bank you want to use from BrawlCustomMusic. For this tutorial, I'll be using http://smashcustommusic.com/9297
Second step is to download it as a nus3bank for any stage. For this tutorial, I'll be using CRS01 - Menu.
Open your nus3bank in any hex editor. For this tutorial, I'll be using HxD.
Scroll down until you find a line that includes the word "JUNK". For the nus3bank I downloaded, the JUNK text starts at 3AB0.
Delete offsets from 0 to the end of the JUNK line. For the nus3bank I downloaded, I will be deleting 0-3ABF.
Select all and copy the remaining hex values.
Next, open the nus3bank of the song you want to replace in your hex editor. For this tutorial, I'll be replacing snd_bgm_BY03_BY_MysteriousDestiny_3DS.nus3bank.
Again, scroll down until you find the JUNK text. For Mysterious Destiny, it starts at 3AD0.
Click the line under the JUNK text (in my case, it would be 3AE0), then paste write your copied values. (Ctrl-B in HxD)
Save your new nus3bank file, add it to your ExtractedRomFS as you would any other nus3bank, then build your CIA.