I pay attention to the color I "sense", either vibrationally or seeing the color myself - no matter what chakra center I'm working with. Just last week, I was giving a Reiki session in the neck area and sensed the color red in that area, which, of course is not the color for the neck area. I'm still not sure how to interpret that, but I just trust the Reiki energy and divine spirit to do what's needed, and in the meantime remind myself that I'm a student of the practice and the Universe. SOmetimes it's important to understand the meaning of the colors we see or sense, and sometimes it's not important to have the understanding. I work under the assumption that if it's important for me to have the understanding, I will receive it.
In other energy healing practices I learned that usually red/root chakra interacts with green/heart; orange/sacral interacts with blue/throat; yellow/solar plexus interacts with purple/third eye. Not a rule, I'm sure, but these are also "complimentary" colors to one another on the "color scale", and I think there is definitely significance in the chakras as well.
If a client reports seeing certain colors, to me it implies that there is work happening in those particular energy centers - BUT - it could also mean that these are strong energy centers in that person. There's just really no "set rules" to energy work!!
For myself, because I have a tendency to analyze every thing, I'm learning to trust the flow of Reiki, instead of attempting to analyze my perceptions. However, at the same time, we ARE students, and part of our own training is to learn to hone our perceptions!!
Sorry to sound so vague - but that's how I see it - for me, anyway!!
Blessings in your learning!!! Namaste...Heart of Grace