yes I use ninhax 2.0 and load my custom themes using 3ds_homemenu_extdadatool but I have no idea on how do I could keep multiple themes. everytime I want to change a theme im replacing the files in this app folder..
Okay, in that case download Custom Home Menu Manager
1. Extract the .zip to the "3ds" directory of your microSD card. It should look like this "Your SD Card/3ds/CHMM/"
2. Create a "Themes" directory to the root of your microSD Card. It should look like this "your SD Card/Themes/"
3. In the "Themes" directory, create a new directory for all your themes and place the .bin and .bcstm and .png files for that theme in it. For example "Your SD Card/Themes/MyTheme1/"
Now the Custom Home Menu Manager will remember that theme forever and if you want to create a new theme, just create a new directory (for example "MyTheme2").
4. To install and switch between themes, open Ninjhax homebrew launcher and choose CHMM!
5. Pick the theme you want and press install, wait a while and press start and shutdown Ninjhax.
6. Enjoy your new theme!