The three large factors that affect the functionality of any shop - of nearly any size - seem to be:
Ability to keep it clean
Mobility of tools to accomodate affore mentioned as well as to streamline production of multiple process' at any given time
Positioning of tools to facilitate immediate use, clean up, and storage - again improving productivity
I run five benches in the shop and each has a purpose (generally none of them being hobby guitar building). Each bench has a storage area underneath for the tools most commonly used at that bench. This allows me to stop toting tools from one end of the shop to the other and localizes my activity, thus allowing me to increase my productivity. I should clarify that I don't own five woodworking benches;
1 torsion box for flat assembly,
1 router bench,
1 "clean" bench for fine work, (would love to turn this into a down draft!)
1 catch all bench that accumulates all the odds and ends tools
1 woodworking bench set up standard with fore vice, tail vice, bench dogs, and stop block
My personal preferance is to mount my benches on castors so they can be easily moved to allow for cleaning, or simply to put them in an order that speeds up my production on any given invoice.
I know this is all pretty basic, but then most of the things we do to increase profit are, so....
Take it easy, and congrats on the new digs.
Nate Robinson