I think you should multi sync your stores then you can manage your stores much easier so you can do a report for them easily. To sync multi-stores, you can try the Multi-store Sync Power app by Egnition. This app has some features that may interest you:
After syncing your stores, you can manage reports from them easily with these 30 Best Shopify report apps.
Hope it's useful for you.
Are you doing dropshipping business or sell your own inventory-products?
If dropshipping, maybe you can use a Shopify dropshipping App to manage multiple Shopify stores in one ShopMaster account.
ShopMaster has a Reports module that can help you know more details of data analysis.