searching for images not in albums?

I'm guessing that when you say "main Photos section" you mean the Library view--what you get when you click on Library in the upper left of the sidebar. Is that correct? The Library view shows your library (duh!), meaning that it shows everything in your Library. What you see there, and how you see it, can't be changed, because that's what it's for.

To display pictures, we use Albums and Smart Albums. Then you get to see just what you want. I have albums for events (like a birthday, maybe) inside of folders for years inside of folders for decades. I also have a folder of folders for things not sorted by year, like all the pictures of my wife's family, for instance, or astronomy pictures, or flowers, etc.

The easy way to collect things is with Smart Folders. I assign keywords to all my pictures that help me find them. All the pictures of my wife have her as a keyword, so I can use a Smart Album like this:

This will make an album with pictures of my wife taken in 2005 and 2006 but not in New Zealand. (I'd get better results if I used her actual name.) If I have new scans of her matching the criteria, they will automatically be added to this smart album-- it's always up to date.

I pretty much never look at the Library View.

I did get kinda lost...

Here is maybe a helpful example: I am sorting several hundred pictures taken by 4 unsynchronized cameras with no GPS, at Warwick castle. I decided to separate them into smaller parts to help sort them.

So I made empty albums that I named Costumes, Upstairs, Downstairs, Dungeon, Entrance, whatever. Then I made a smart album that was like Album=is=Warwick AND Album=is not=Upstairs AND Album=is not=Downstairs, etc. This album had all the pictures, since those other albums were all empty. Then in it I'd find some Upstairs pictures, drag them to the Upstairs album, then drag some Costume pictures, then find some more Upstairs pictures, etc. The working Smart Album gets fewer and fewer pictures, so it gets easier.

Anyway, that's one way to go about it.

Folder is not a choice in Smart Albums.

(Smart Albums are also not a choice for Smart Albums-- you'd end up with infinite feedback loops. )

But this is where you use keywords. In every one of my albums I select all and add the name of the album as a keyword. You can do the same for folders.

You'd have keywords of ProjA, ProjB, Pers1, etc, and Project and Personal. A picture that's in two or more albums will have all the keywords for all the albums it's in. So a picture might have keywords Personal & Pers2, so you could find all the Pers2 pictures, or all the Per2 pictures, or all the Personal pictures.

And keep in mind that an album doesn't contain pictures. When you "put a picture into an album," its name is added to a list of pictures to display when the album is clicked. So two albums can both have the same picture name in their lists, and that picture will show up when you click either album. And when you delete a picture from an album (removing its name from the list), the picture's name remains in the lists of other albums. 

So albums give a specific view of your pictures. My "Grand Canyon" album, for instance, offers a view of pictures taken on various trips to the Grand Canyon, and my "2012 Trip to California" album shows the pictures on that trip, some of which are the same pictures as shown in the Grand Canyon album-- the picture's name is on both lists. 

The Library View shows all of the pictures in the entire Library. You can't remove a picture from the Library View without deleting it entirely.

Create a smart album with:

Album is not any