Gemstones are always energised. Some need clearing, so bury them in a house plant or in your garden. Earth is its natural habitat. Plants love gemstone energy. Do it between new moon's or full moons. Also, communicate with your gemstones. Let them know who you are. Ask your gemstones what they can teach you.
Amethyst heals the root, heart and 3rd eye chakras. Rose quartz heals heart (compassion). Meditate with them or sleep with them next to your bed. Wearing them is always good. However you choose, the gemstones will strengthen the chakra its connected to.
I am a big found of sound resonance clearing. IE- using bells, or music to essentially reset the vibration of the stone. One of my favorite things ponder and watch is Cymatic sound experiments. (you can view an example here if you aren't familiar! https://www.youtube.com/watch?v=GtiSCBXbHAg ) I am also an air sign, so this method really resonates with me! Bonus, that its super fast.
Lots of people like to place them out during a full moon.
You can also place them with other high vibration stones like selenite, or kyanite that will "retune them"
You can place them in a dish of salt or salt water, as long as the mohs hardness is a 7 or above. This is perfectly safe for the quartz your talking about, (depending on if there is metal on the necklace) but not for all stones.
Use whatever resonates with you, and you will be pleased!