There are two main ways for placement of Crystal and gemstones on chakras.
a.) Placement on a single chakra at a time
Single chakra therapy is to take a single stone and sequentially  work your way up the.chakras. i.e. place suggested stone  on your  root chakra; then  on your Hara chakra so  on, giving Reiki for 3-5 minutes on each chakra

b.)  Placement on all chakras at one time
Place 7 clear quartzs or recommended stones on all your chakras - starting at the base chakra and working your way up. Let them stay on your chakras for 5-25 minutes. And give Reiki.
Remove the stones in the opposite order - starting from the crown chakra.
If a stone makes you very uncomfortable, it is advisable to remove it.
One can experiment to see what works best for them.
One can always substitute clear quartz for any chakra.
Different healers have different charts.
Experiment and find what works best for you.

Seven Major Chakras

First: Root Chakra (Muladhara)
Second: Hara Chakra (Swadhishthana)
Third: Solar Plexus (Manipura)
Fourth: Heart Chakra (Anahata)
Fifth: Throat Chakra (Vishuddha)
Sixth: Third Eye (Ajna Chakra)
Seventh: Crown Chakra (Sahasrar)

However, here are some stones that are recommended on each chakra.

First Root Chakra (Muladhara) Colour : Red
        Gemstones
        Red Garnet
        Red Jasper
        Smoky Quartz.
        Black Obsidian
Second Hara Chakra (Swadhishthana) Colour : Orange
        Gemstones
        Carnelian
        Orange Calcite
        Tiger’sEye
Third Solar Plexus Chakra (Manipura) Colour : Yellow
        Gemstones
        Citrine
        Yellow Tourmaline
        Yellow Aventurine
        Topaz Golden Calcite
Fourth Heart Chakra (Anahata) Colour : Green
        Gemstones
        Rose Quartz
        Kunzite
        Watermelon
        Tourmaline
        Jade
        Adventurine
Fifth Throat Chakra (Vishuddha) Colour : Blue
        Gemstones
        Aquamarine
        Azurite
        Sodalite
        Purple Rainbow Fluorite
Sixth Third Eye Chakra (Ajna) Colour : Indigo
        Gemstones
        Lapis
        Blue Fluorite
        Sugilite
        Clear Quartz
        Blue Lace Agate
        Amethyst
        Aquamarine
Seventh Crown Chakra (Sahasrar) Colour : Violet
        Gemstones
        Amethyst
        Oregon Opal
        Clear Quartz