Each photo is in one Event and stays there (what you're calling the "main" album, I think). Each photo may also appear in one or more Albums, but the "photos" in Albums are really just links (or pointers, or aliases, or references) to the actual photo in its Event.
So, when you delete a "photo" (actually an alias) from an Album, it just disappears from that Album, but stays in the Event. When you delete a photo from an Event, the photo file is deleted from the iPhoto Library, and all of its aliases disappear from from each Album that it appeared in.
When you "put" a photo into an Album, I'm not sure why you don't want it to also show in the Event list? Perhaps you want to organize all the photos into albums, and you want an easy way to see which photos haven't been organized yet?
If this is the case, I would make a "Smart Album" that shows all photos that are NOT already in an album. When you drag a "photo" from such a Smart Album, it will disappear from the Smart Album and show up in the new Album.
To make one, go to File-->New Smart Album... give it a name like "Unsorted Photos". Match the following condition: "Album" "is not" "Any" and click OK. Now Unsorted Photos will contain all photos (actually aliases of all photos) whose album field is not any of the ones in the dropdown list.
Hope this helps.