Kevin, I would highly recommend QuickBooks Online or Xero as your accounting software. Both have ability to work well with the Shopif inventory and have awesome features. You will need the help of Shopify addons when you feel the need to automate the inventory update between Shopify and accounting software. Top apps sorter by popularity and rating here
In my research of 1000s of top stores, QuickBooks Online and Xero were by far the top choices for accounting. Hope this helps.