I am going to repeat what others have said and add my own comments too.
PANEL
First of all where will your panel be set? Make sure you get a panel large enough to expand. Place the panel as close as you can to the areas that are going to have the most circuits, this will help in keeping you wire costs down. Stay away from panels that don't except quad beakers or are difficult to find. Murray and Cuttler-Hammer are good choices and there are others too. Quad and split breakers allow you to install two or four circuit breakers in the space of one or two.
You may have to have these outlets protected by GFCI, check with your local code jurisdiction.
WIRE TYPE AND SIZE
I can see you using either romex or surface mounted conduit in your shop, hopefully you placed some well located conduits underground that come up in your walls. If not, you may have to use a combination of both. MC cable is also an option if your code jurisdiction allows it. I agree that #12 should be used for your outlets, especially if you are in an area that will have heavy tool use. #14 can be used as convenience outlets where an occasional tool or battery charger will be plugged in.
OUTLETS AND THEIR LOCATIONS
Depending on what type of use you expect at each outlet will determine how many outlets should be tied to one breaker. For example, if you are going to have a work bench, I like to have at least two dedicated circuits in this area for power tool use. I also like to make these double duplex so that you can plug in your battery chargers and still have an outlet available to plug in your tools or radio.
Set your outlets above the work bench (work bench can be anywhere from 31" - 36" with a 4" splash in some cases) I like to have a welder outlet close to the door so that my welding can be done outside when possible and avoiding a large extension cord which are not only costly but heavy and difficult to store too. Be sure to have at least one outlet outside for a power washer or other tools and equipment.
Put a couple of outlets in the ceiling so as to avoid tripping on cords. Place convenience outlets about every six feet and on every wall, including the one between the two roll up doors. These outlets can be on one circuit, keep them under 8 outlets per circuit (I usually have no more than four per circuit)
Place an outlet for your irrigation system if you intend to have one.
Place a few outlets higher on the wall if you intend to plug in some neon signs or other items.
LIGHTING
Plan on using T-8 light fixtures. They are readily available and the cost is reasonable. Buy these from and electrical supply house. If you choose to get the four lamp lights, get them with two ballasts so that you can switch them for two level lighting. I would place them on both sides of the bay, this will avoid the light being directly over the car, making it difficult to see when working on the engine or under the hood. I like to use HO F96 lights in high work areas, but that is my preference.
Two lamp fixtures are fine for areas that don't need a lot of lighting.
Place at least one four lamp fixture over the work bench area, you can make this an individual switch or make it a 3 way switch and locate the other switch near the others at the door. This allows you to adjust your lighting needs and conserve energy too.
Make sure that you run three way switching if you have more that one entrance. Set up your switches in a way that best suits your needs. I like to have both low level and working light systems.
Plan on having outside lights near the doors. Some like to have them on sensors others like to have them on switches, so it is important to decide what type you like and wire accordingly. If you intend on working outside the shop, place a HID light in the area you are considering working. This should be on it' own switch.
You should be able to run all of your lights on one 15 amp circuit, if you have less than 12 fluorescent 4 lamp light fixtures.
I use spec 41 lamps, but now is the time for you to select the color of light you want for this area. Spec 41 lamps are brighter.
UPSTAIRS
Is this considered residential use? Follow local code on placement of outlets. Switching should be for both overhead and outlets (lamps)
Recessed lighting is nice and comes already configured for fluorescent lights if you want. I prefer 5" lights over the 6". If you are putting these in an insulated ceiling, these are the two sizes that come in IC protected and are approved for this use. I would avoid low voltage lighting, it is expensive and can be a pain.
Remember to run a communication line and a TV cable to the areas that you will want to have your set up (you may move it, so plan for that now) Install a double duplex outlet near the TV set for multiple hook ups.