Hey Saurav,
There is a Government tourism office near the bus stand of Shillong. From there daily buses go to all points in Meghalaya (drop you back at Shillong in the evening). It will take 4-6 days to cover almost all Meghalaya. You just book tickets to Guwahati; from there take a sharing jeep to Shillong and stay in a hotel near the bus stand or Police bazaar of Shillong. I visited there in April 2018 so you can ask any query related to above.
Happy travelling!!!!!!