A bit of introduction:
!!APKs / JARs are just glorified zip files!!
so it all depends on the base you are working on . Basically it comes down to this. if your odexed base has inside any APK / JAR a dex file then you are good to go . else stop here.
how do you check that? as i said jar / apk are just glorified zip files so take a peek inside the apk/jar with your favorite archive program
m8 base has this already so all is fine.
so what to do next?
easy. just delete all *.odex files from app / priv-app / framework . surprise all is done . your rom is deodexed and ART compliant.
sure you can go and decompile any apks/ jars with apktool / baksmali depending on your needs and change code / add / delete whatever you want. just make sure your edits are byte code compatible, otherwise it will break ART compiler.
P.S. as the title says this is a TIP, not a guide for you to follow blindly. should be enough to put you on the right track
P.S.2 if you are confused, not my problem since this is for rom owners you should know what your doing. if not maybe you should stop making roms