Is the practice associated with a specific civilization that started it before others? Is there any reason in particular we believe they started the practice? I'm generally interested in the history of makeup if anyone can enlighten me.
The first known use of lipstick was in ancient Mesopotamia, around 2500 BC.
As for fingernail polish/paint, the Chinese are usually credited with being the first known users of that type of makeup, going back to about 3000 BC, though the Egyptians were also believed to be doing it around that time period as well.
The idea of highlighting/coloring ones lips or fingernails could very possibly be older than that, so I say known users because that timeline is when we have the earliest archaeological evidence of those types of makeup being utilized. As to why this practice originated, it is speculated that it was done back then largely for decorative/cosmetic purposes to better highlight those areas of the body (as it still is today), with different shades of color being chosen depending on the social class of the person wearing that makeup. In Egypt for example, it is believed that bright red shading was used to signify a person of high status or royalty. Some warriors also painted their nails as a symbol of status or rank.
Here is a link to a decent book that deals with the historical use of makeup that you might be interested in.