You can use
Lenan's YATA mod to create your themes. Make sure you use the "Save for 3DS" option when you're done editing your theme or you'll end up with inverted colors. It's a little buggy--especially the color palette editor--but it gets the job done.
In order to get sounds working with your theme you need to use
xextil's Custom Theme Cwavs. You can refer to the topic on what format your files need to be in for your sound effects to work, but the tool you'll need to convert your files is obtained illegally, so you'll need to figure out
what and
how to get it. I know it's a pain, but it's against the rules--and illegal--to share it.
As for converting your themes into a CIA--I don't know, exactly. It can be done and I remember reading about it somewhere, but I'd personally rather not go through the trouble. CHMM is easy to use and very convenient as it is. Anyway, look it up and I'm sure you'll find out more information.
Lastly, be sure to back up your theme cache
before experimenting with themes. You can temporarily brick your 3DS by corrupting the theme cache, which prevents you from booting into the home menu and subsequently SysNAND/EmuNAND. Backup your theme's cache in your exdata folder: EUR "000002ce", USA "000002cd", JPN "000002cc" Restore it if--
when--you run into any problems.
Those are pretty much the basics.