Not knowing your equipment it is a little difficult to guide but I'm currently setting up my studio and here are a few things I've done plus pointers I've gotten from others.
1) Separate your work areas if possible. Ideally you would want separate areas for the following:
a) Cutting/design/prep
b) Cold working and all grinding equipment
c) Sandblasting area (Keep this away from all things wet if possible. If your sand gets wet it won't flow)
d) Spray area (if you use mica's, Spray A, etc.)
e) Office area
f) Photo area
g) Kiln shelf prep/clean area
2) Good lighting. Natural where you can. I have ceiling lights but I also have 8' fluorescent lights hung right above all work area's.
3) HEPA vacuum for cleaning kiln, dust and all things of powdered glass. Along with this comes good eye and ear and nose protection. Wear that respirator in all grinding activities and when cleaning shelves with used fiberpaper/thinfire.
4) As mentioned, rubber floor mats in all areas where you spend any length of time standing. Your feet and your back will like you for it.
5) Lots of outlets, GFI protected in areas where you work with water (grinders, WBS, etc.)
6) Sump all of your cleaning into buckets except maybe your final rinse and clean. You don't want powdered glass going down the drain.
7) Access to a hose if possible to clean the floor down, wash off things, etc. It's a messy job as they say.
8 If you have the opportunity to seal or paint your garage floor before you get too many things set up it is a good idea. Professional epoxy jobs are pretty expensive, up to $2 - $3/sqft. You can get a reasonable water based epoxy for concrete at Lowe's made by Rustoleum for about $50 that will cover 250 sqft. This will help in cleaning later on.
9) Glass racks. Don't make them too high. I made mine out of 3/4" plywood. You want the bin's at least 6" x 25" x 36" (WxHxL) to accomodate a full sheet of glass (assume you use BE). If not you will want to make your racks large enough to safely hold the number of sheets you expect to have at any time. I got cheap indoor/outdoor carpet and glued that to the bottom of the bins to keep the glass from chipping when I slide it in and out of the bins. You should not have to hold glass over your head to put into or take out of a glass bin. (Do as I say, not as I did.......I didn't find out about this until after I built my bins). The reason for this is if you happen to have a poorly annealed sheet of glass or a stressed or hairline fractured sheet it could crack over your head and shower you with shards which is probably not a good thing.
10) LOTS of storage bins. Depending upon what your work is like these will come in various shapes and sizes. I use lots of frits as well as sheets so I built a "mailbox" type of rack on the back of my workbench that stores all of my frits. I can see all of my colors and types very easily. I use the little drawer holders like you see for workbenches for all of my small scrap and I got larger bins at Staples on wheels for my larger pieces.
11) Wheels are your friend. The more things you can make mobile, the better. It allows you to clean better, change your configuration, etc.
12) Last but probably most important is TUNES...

.....If you are like me I GOTS to have my tunes when I'm working!!!!!!!
Good luck,
Phil