As a simple rule of a thumb for beginners – you can choose the gemstone for balancing the specific chakra by its color:
red chakra stones are used for the root chakra,
orange for the sacral chakra,
yellow for solar plexus chakra,
green and pink for the heart chakra,
blue for throat chakra,
dark blue and indigo for the third eye chakra,
and purple, white, and transparent for the crown chakra.
There are exceptions to this rule, and you will learn best from your own experience once you actually start using the gemstones and connect with them. Most people who work with chakra stones learn to feel their energy, and they relate to them much as to living beings. This is the best relationship you can form with your gemstones in order to learn from them about how to use them.