Remove any debris from inside the crack or hole with a chisel. Scrape the debris away. If necessary, insert your hand or fingers into the crack to brush away more debris.
Mix the mortar in a bucket. Follow the package instructions regarding the amount of water needed. Mortar mix sets quickly, usually within 30 minutes to an hour. Do not mix it until you are ready to begin.
Fill in the cracks with the mortar mix. For large cracks, use a masonry trowel to scoop the mortar mix out of the bucket and spread it over the crack. For deep cracks or holes, use the trowel to put the mortar inside the crack. Tiny cracks can be repaired by spreading the mortar mix on by hand -- but you will need to wear latex gloves. Do not get mortar mix on your bare skin. Let the mortar set until it is hard.
Hide the patched areas with exterior latex paint. It is difficult to perfectly match the color of the limestone with the mortar mix. If the difference bothers you, paint the foundation with exterior latex paint.