Old, I got this off of a tire site for you.
My OEM Bridgestones have a yellow dot located near the valve stems. Going to replace the rear tire soon (with a Michelin Commander II). Should the new tire have a mark that is supposed to be located near the valve stem?
The colored dots are supposed to line up next to the air valve on SOME wheels. Specifically, placing the heavy spot of the tire at this lighter spot will help balance the wheel before adding weights. Sometimes the valve hole indicates the lighter spot but more recently it does not.
On wheels where the air valve can be located at any position on the rim (usually STEEL rims only and some alloy rims), the valve hole can be drilled at the low/light spot on the rim or the heavy spot to try and "lighten" it and balance it.
Although most alloy rims have the air valve in a specific place on every rim the air valve can sometimes still locate the lighter spot on the rim. On cheaper not-so-well-engineered rims the drilling of the valve hole will create an imbalanced condition (removing material makes it lighter) so this area becomes the lighter spot.
On higher quality rims the drilling of the valve hole is taken into account and a similar amount of material is removed from the opposite side of the wheel. Therefore the valve hole is no indicator at all of the light or heavy spot on the rim. These rims are sometimes marked with a dot the same way the tires are marked.
Red dot = high point in roundness (heavy spot)
Yellow dot = light point in balance (light spot)
Red is mounted first ("RED RULES"). If you have a low point mark on the rim (i.e. valve stem on steel, aluminum wheels or if the valve stem is in different places on the alloy wheels) then it is positioned there with it. A lot of current alloy wheels also have the stem in a certain place because of the design or a dimple or paint spot on the back of some alloy wheels.
If you don't have a low spot marker then mount using the balance marker. If your rim is not machined out to counteract the drilling of the valve hole and it is drilled in a specific place because of the wheel design then this may be the lightest point. Then the yellow dot is mounted 180 degrees from this.
It's really difficult to know what the wheel manufacturers intended without finding the specifics of the wheel you are working with. The tires are a little easier to work with especially since each manufacturer releases technical information to shops.
All this aside any reputable tire shop will know how to mount and balance your tires correctly and mark them accordingly if you need that done for identification purposes afterwards.