Agree with @fromlostdays stick to retroarch as much as you can, you setup your controller once in the main interface, and can then tweak it for different cores if needed, much easier than separate emulators for everything which all need controller configuration. Also the retroarch cores are updated regularly, which cant be said for some stand alone emulators, some havnt been updated in years.
In bigbox you can toggle a "use all controllers" checkbox, which should do what you want.
Skipping prototypes etc. cant be used for platforms other than mame/arcade. However there is a new combine feature that will consolidate those games as long as the name is the same, for example super Mario bros, super Mario bros (proto) super Mario bros(beta) should all be under the same game, this is checked by default on import, but can of course be unchecked.
If I'm understanding your edit correctly you can click on 1 game, then ctrl a to highlight them all, right click then delete. this will remove them from launchbox.
Hope this helps, any more questions feel free to ask.