My reiki training included a great deal of additional training in chakra work, so I incorporate the two most of the time. I find that the two modalities work well together. It is very common for me to work with clients who are familiar with the chakras. I ask them to visualize the chakra that I am working near as a tool to determine the health of the chakra. I also use a pendulum quite a bit, too.
However, in my reiki classes, I am careful to distinguish between what is Reiki and what are "add-ons". I don't even get into the "add-ons" until Reiki II to avoid confusion.
Herbmom