True to the bold part.
If you want to put a stadium at the place of an already existing stadium you should get the id of the particular stadium, edit the name (also inside glares.lnx files) of the files of your custom stadium to match that id, put your name edited files in the appropriate game folders (data/scenassets/stadium or fx or crowdplacement) replace if asked. Go to CM16 load your DB then regenerate (you can regenerate with the tool of your choice). Start the game, the old EA stadium should be replaced by your custom one. Warning: This works with most EA ids but not all. Some newer stadium come with radiosity file, using those ids would cause game crash at day time. If you replace mostly generic stadium you are safe.
If you want to add a stadium with a new id, you need to open CM16, load your db, go to the stadium icon, select a stadium that you will use a base, click clone, select your id (I tend to prefer using the id proposed by cm16), edit the stadium informations to your liking, save, go to the team icon, select the team for which you want to assign the stadium, click the refresh icon, assign the stadium to your team, save. Do not close cm16 (you can but why closing it to reopen it just after?). Now edit the files names of your custom stadium to match the id you picked in cm16 (don't forget the glares.lnx files) and like mentioned above put the file with the edited name in the appropriate game folder, replace when asked. Go back to CM16 regenerate and you are good to go. In game, reset the squad in the custom team section, go to profile, save squad. Warning: 1) Depending on the stadium you will use as a base to clone, .rad file might be generated in the data/sceneassets/radiosity folder, delete any file you will find in this folder (if it exists) before regnerating (if you did regenerate before noticing the presence of this file simply regenerate after deleting them.). Those files would cause game crash otherwise. 2) New ids do not have proper night atmosphere and lightning, no solution has been found yet. But three "ghost" EA ids exist (they do not correspond to stadium in game), 174, 177 and 225. If you select one of this id the corresponding stadium will have proper night lightning and atmosphere.