How to delete/edit apk's in Marshmallow zips

I am very familiar with Android, being a user for the past 4 yrs. I recently got mine back, COMING FROM AN IPHONE blehhh, thank God! I was so used to KitKat editing zips left and right from folders using Winwar. Now on marshmallow it seems that all zips are compressed a bit more or hiding somewhere. On Aosp roms they normally include the phone.apk and contacts.apk and want to delete them and use the Google ones. Need info on how to and what to delete and not mess things up. I can use either RootExplorer or Winwar. Please let a brotha know.

Thanks

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