A different interpretation of the question gives a different answer...
If you are using a dodge/burn layer, and you are drawing into it, then yes, your foreground/background brush colours to make a difference to the result. Generally, when burning, use black to burn, and white to un-burn. When dodging, use white to dodge and black to undodge. I normally set the brush foreground colour to black and the background to white for burning. For dodging, switch them around. Then you have the left mouse button to dodge or burn, and the right mouse button to undo.
You can get different results with different colours. Burning to black gives the normal burn result. Burning to a colour will burn toward the colour you use, so will tint the result.
Burning is not quite the same as multiply by the way, so if you have a true burn capability, you should use that rather than multiply.
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