Here's a simple Photoshop technique to convert an image to sepia, and paint spots of color back into it.
1) Open your image file In Photoshop, and select Image>Adjustments>Desaturate to remove all color from the image. The image should be still RGB.
2) Your image will now appear in black & white.
3) Go to Image>Adjustments>Photo Filter, and choose Sepia. In the Sepia dialog box, Adjust Density to your liking and also check Luminosity. Click OK when you're satisfied with the sepia image.
4) Select the History brush from the tool palette. Choose a brush size appropriate to the spots you've chosen to color in, using the palette located just under the file menu bar. The brush hardness should be 100%.
5) Using the History brush you can now “paint” the color back where you want it. Don't paint all in one stroke, but stop and go so you can undo any errors without having to start all over again.
6) Continue the process until the area is complete. Save.