If it's two day plan I would say to plan for Cherrapunji and Dawki river. Stay in Shillong from there you can book taxi to book the places.
Day 1: Shillong - Cherrapunji - Shillong
place to see Elephant Falls. On reaching Cherrapunjee you can visit Arwah Cave, Noh-Ka-Likai Falls, Mawsmai Cave.
Day 2 : Shillong - Dawki - Shillong
Visit cleanest village in Asia- Mawlynnong. On reaching Mawlynnong you can visit The Village, Balancing Rock and Living Root Bridge. Later drive to Dawki. Here you can enjoy boating in the crystal clear river Umngot. Later visit the Indo-Bangladesh border.
Note : If your total trip is only for two days then you can plan as per Day 2.
If you really want to enjoy the amazing weather and nature of Meghalaya just book a taxi from guwahati, for 2 days he will take you to all the major points, shillong, cherrapunji, dawki, and try to stay in sohra for a night you will love the peace and beauty.