These themes looks amazing. :D Are you sure you guys are beginners? ;)
Nice work on TWRP. Just wanted to put that out there,
As of I know you can make a flashable zip to flash Boot.img trough recovery. Here is the updater-script for only Boot.img that I found
I found a good website called pimpmymiui. Just google it. Full of great themes and they look like they work with this ROM.