Hi Sue,
Ok, this is a bit long. Organizing is putting like things together and having a place for everything with things used a lot that are easily accessible. Keep frequently used items visible and handy and less used items in a place where you know and can access.
I would first start with your fabric. I would do the fabric folding over the ruler as found in a tutorial here at QB. Put the fabric together by fabric type and then in color groups. The fabric ends up being all similar sizes. This may take a while but everyone who takes the time to do this has been very pleased with the results.
I would use small clear plastic containers for keeping smaller items. Put a label on the outside, even if only a piece of paper taped to the side of the container. The dollar store has shoe box containers that can be stacked together on the closet shelves (the tops are not clear but that's ok).
Once you sort through everything and see what you have, then you can determine the size of containers, etc. that you will need to keep like things together, such as thread, binding, tools, etc.
If you are on the go alot and have waiting time you might want to think about putting together a small take-along project bag. (Bag, tote, large purse, etc) This could be the time that you have a project for hand work such as a GFG, Grandmother's Flower Garden. These work well for using up small scraps of fabric.
There is also another section about how to cut, handle and store fabric scraps. To start I would just find one large plastic container to keep all scraps together in one place.
For your rulers, there are several threads that talk about rulers and their storage. Some have storage boards that hang on the wall and others have a board that sits on a table. There is also new hangers that will hang like a clothes hanger that hold several rulers. You may also be able to find a small container to keep them all together other than maybe a very long ruler that you could then hang on the back of the closet door or on a wall grouped with other sewing items.
I would keep a list of the rulers you do have, along with other sewing tools, even noting when you have duplicates.
If you go to classes or quilt club meetings where they sew some quilters have a whole separate rolling tote that has a second set of all the tools they use so that all they need to do is to drop in the sewing machine to be ready to go to class. There are even some who have a machine just for classes.
You may actually be glad that you have deep shelves. Stand the taller items in the back of the shelf and then put smaller items in front. Lighter weight items will be at the top and upper shelves with heavier items at the bottom. I would put items not used very much on the very top shelves. Usually the top shelves take having a step stool to get to, at least for me as I'm a short person.
You may actually find that you have room to keep your sewing machine(s) on the bottom shelves when not in use.
Once you get all of the above completed ask again if you need additional advice for getting organized.
Hope this long instruction explanation helps. Good Luck!
Pam M