So I can use ninjhax to install custom themes on my 4.2 sysnand but I would prefer to install via a .cia, is there a easy way to throw themes into a .cia?
Yes, there's a way, but the best way to install themes is with CHMM: https://gbatemp.net/threads/chmm-custom-homemenu-manager.379349/
It does come as a cia. Note that themes are not a feature of 4.2...

