Sometimes new holes are needed to add the new hardware. I have tried a few different products and techniques to fill holes but always had the old holes still showing through. After asking around other RT vendors and personal experimenting, I came up with a technique that I like the best.
Then I mix up a batch of this Minwax wood filler (a product called Bondo works just the same). You will need to do this in a very well ventilated are because this stuff STINKS.
You can be done or repeat after this step but I like to finish off with this stainable wood filler also by Minwax, this is ready to use and no odor.