Wood fillers, by their nature don't stain well after dry. They harden & seal up. Your best results, from my experience, will be by coloring the filler before it has set up. With all the products out there, my favorite is one I learned about way back in wood shop. Durham's Water putty. It's a powder that you mix w/ water just before using. You can add acrylic or powder paints to color match to what you need when you mix it. I get it at my local hardware store. One can is probably a lifetime supply. Since you only mix what you need, the rest lasts forever if you keep the can closed. Small bottles of acrylic paint or powder paints are available at hobby or craft stores. Practice on some scraps to get the correct tone.