How to reconcile Shopify and Paypal transactions for accrual accounting?

[kpauli]

I am in the accounting department and new to Shopify. I am trying to get an understanding of what reports to use for accrual accounting. 

1. Do ALL transactions run through Shopify?  
2. Do I need to get additional reporting data from Paypal?
3. What reports are recommended to use in Shopify and/or Paypal?

From what I am running into, it doesn't seem that the numbers match up between Shopify and Paypal.  I am told that all refunds are through Shopify, but some refunds on Paypal I am not seeing in Shopify.

Any insight would be greatly appreciated!!