Hello Nini,
The task at hand can be overwhelming or fun....that's up to you. I hope you start out with everything in boxes or crates or whatever....because all of that should just be in some remote area of your home like the garage or in the far corner of your new sewing space. Beforehand, take the time to paint the room your favorite choice of color. Set up your furniture, sewing table, etc. in the places where you think they will best work for you. This might take some moving about until it feels right for your needs. Dress up your windows with something that suits your taste.
Now is the time to fill it up...one bag/box/crate at a time! And be sure to take your time. With a new setup, maybe you want to show your fabrics on comic boards. Doing a bit of fussy folding now will make your room look just like that quaint little quilt store you love to shop in! Am I sounding a bit corny? Perhaps, but I've just recently done exactly that, and I couldn't be more happy with the results.
Take the time to sort your stash by color (mine looks like a very long continuous rainbow on my purchased Ikea bookcases). Lights to darks...another shelf has Hawaiian prints (my personal obsession!) then, 4th of July/Halloween/Christmas prints. It's all about the organization!
This time you take will all be worth your efforts once it's complete. As for small items like tools, bobbins, shears, etc, I use kitchen drawer dividers to keep those things in check. A pegboard holds my templates and rulers. Shoeboxes in clear plastic hold fat quarters, jelly rolls and pattern envelopes. Our dollar store has a plethora of organizational goodies at reasonable prices. You can choose clear or varied colors. Mine are apple green and turquoise. Have fun with it and let us know how you progress!