If the flooring is on the dark side, you can try taking some LIGHT filler, and roll it around in your fingers with the stain that closest matches your flooring. Henry is right in that the filler doesn't take to stain very well. This is especially true when the filler has dried and hardened. When it's soft, it will take to stain a little so work the stain into the putter by rolling it around between your fingers or palm. Only work with what you're putting down. In other words, don't take a large 'dab' to color and just think you can take a tiny bit off the 'dab' each time you want to fill a hole. It's best to work with as little filler as possible at one time, and that's done on a per-hole basis.