I had a researcher contact me who was looking for help sorting out his American Indian and African (black) ancestors. To complicate matters, many of his ancestors were from the State of Virginia, and parts of what was later West Virginia. Of course the earliest records just divided people into white, free persons of color, and slave. So bear in mind in your research that a reference to a "Free person of Color" in the 1700s or early 1800s, many were Native American; but, there were also many free blacks.
In later census records when race was listed as white, black, mulatto, Indian, etc., people often presume that if the head of household is listed as a mulatto and they owned slaves, then the head of household was most likely Indian. While this is sometimes the case, there are also documented records of blacks who owned slaves, so the word mulatto will not necessarily be an aid.
The main problem is the change in the meaning of words over time. For example, in Colonial times the word mulatto did not refer to African mixed bloods. It referred to whites who had intermarried with Natives. It wasn't until the mid-1800s that the word mulatto began to have a different meaning due to changes in verbal usage.
To complicate matters more, the State of Virginia decided early on that there were no more Indians within the state. It was not to their benefit to have Indians, as particular treaties would have to honored. Moving into the late-1800s and even as late as the 1940s, anyone not listed as white was listed as black or Negro—even a full-blood Native American. The result is that many researchers think they have found a black ancestor in their family tree. African Americans tracing Native ancestry also have to face this problem—was a particular ancestor actually black, or were they Native? In 1924, the state passed its "racial integrity act." This was a prohibition on inter-racial marriages. Here is an excerpt from act:
It shall hereafter be unlawful for any white person in this State to marry any save a white person, or a person with no other admixture of blood than white and American Indian. For the purpose of this act, the term "white person" shall apply only to the person who has no trace whatsoever of any blood other than Caucasian; but persons who have one-sixteenth or less of the blood of the American Indian and have no other non-Caucasic blood shall be deemed to be white persons. All laws heretofore passed and now in effect regarding the intermarriage of white and colored persons shall apply to marriages prohibited by this act.
If you read closely, you'll see that a person with one-sixteenth or less American Indian blood was considered white. But, if they had more than one-sixteenth American Indian blood, they were considered black. This also means that some people with Native ancestry were listed as white on census records. About the only way to sort this out with some degree of accuracy would be to get a DNA test; but, even that may fail to clear up the issue, particularly for blacks searching American Indian ancestry. Having both blood lines show up in a DNA test will not tell them which ancestor unless a direct line of descendants can be tested also.
As you can see, the genealogical road you are traveling will be filled with bumps, potholes and detours. Try to hang in there. Trace family back as far as possible, for that is where you will most likely find the truth. Gather as many court records as possible, including probate and tax records; and, be sure to read as many historical records as possible on the area where your ancestor lived. Anyone of them may provide your answer. All this being said, the State of Virginia has some great archives, some of which are online. A good resource and starting point for West Virginia is: http://www.wvculture.org/history/index.html