Your photos are not scattered throughout the program at all. You are just fundamentally misunderstanding iPhoto.
You have a one library of photos. That's it. Everything else you see there -- albums, events, Faces, Places -- are just different criteria for viewing the same photos. Events is the photos grouped by time. Photos is the images grouped roughly by when they were imported into iPhoto (and you can turn off those "headers" by de-selecting "Event Titles" in the View menu). The photos view can be re-organized *ANY WAY YOU WANT,* even entirely manually.
To put this another way, in iTunes you can see songs by song name, by album name, by artist, by length and a dozen other criteria -- but it's all the same library of songs. In iTunes, songs are actually organised (on the disk) by Artist -> Album -> Song, regardless of whatever way you are looking at them. Likewise, in iPhoto photos are ACTUALLY organized by EXIF info regardless of how you are looking at them. The program just gives you options to look at your photos however you want, and most people don't want to stick to just one way. Sometimes you are looking for pictures from your Paris trip, sometimes you are looking for photos featuring Aunt Betty, and sometimes you are looking for photos from 1999. So iPhoto can show you a subset of the library that matches any of those criteria and many others.
iPhoto does not provide for way to "turn off" or "hide" the Events, Faces and Places views, but you're not obligated to use them. As you've already learned, you can create "albums" that show only photos hand-picked by you to meet a given criteria without regard to dates, faces, places etc., and you can use the Photos view to see your photos in whatever order you wish (you can also use both Albums and Smart Albums to "subset" things in various ways). The program *also* lets you organize photos by almost any criteria you want as well. It just *also* keeps track of the photos by other criteria (Events, Faces, Places) for those occasions when you might need to find something by those criteria (and in the case of Faces and Places, doesn't actually do anything until you set that up!).
I hope that helps you understand it better.