I have been finishing cabinets for over 20 years. The best way I have found to patch small holes is as follows...
If you are going to use a stain, apply that first. Afterwards, apply one coat of your chosen finish. This will give you the true color. Colored putties are generally sold right next to the stains and clear finishes at most stores. Pick a color or colors that are close to your finish color and mix them together until you get a match. You may have to fill a hole or two to see if it's right. If it,s not quite right, use a pin to dig it out and try again.
Fill the holes-by pushing in the putty and try not to leave any residue around the holes. When you get the right match, apply one or more top coats over the entire stock.
If you are going to use a stain, apply that first. Afterwards, apply one coat of your chosen finish. This will give you the true color. Colored putties are generally sold right next to the stains and clear finishes at most stores. Pick a color or colors that are close to your finish color and mix them together until you get a match. You may have to fill a hole or two to see if it's right. If it,s not quite right, use a pin to dig it out and try again.
Fill the holes-by pushing in the putty and try not to leave any residue around the holes. When you get the right match, apply one or more top coats over the entire stock.