Are you wanting to add objects' areas only of a certain color?
If so, then just include the color in your selection filter.
Or maybe you want to add the area of objects with certain colors and subtract objects with other colors.
When you say color do you mean objects with color overrides, or do you mean objects whose layers are certain colors, or both?
If you want to both add and subtract in the same AREA command, then you will have to process the selection set of all objects being considered and keep the command running object by object with "Add" or "Subtract" responses within.
OR, you could process the selection set to subdivide into a second selection set thereby having a set of adds and a set of subtracts. But I'm forgetting how the command works and my AutoCAD isn't running.
I personally wouldn't use the AREA command, but process the selection set by acquiring each 'Area property and adding to a Plus value or a Minus value depending on color. It can get slightly more complicated if you want to enter multiple colors in your (getstring) function, but we have an answer for that if you don't have a method already. Then again you could ask for colors separately via (while (setq color (getint ...)...) ...) and create a list of them, which you would need anyway.