Are you using the free app from the Shopify app store?
Check out www.eBridgeConnections.com
They have a robust QuickBooks integration tool. Or they have a Sage 50 to Shopify app for 99$/month.
They've been great at helping me setup multi-language Shopify store invoices at the start, as I'm not a very technical person.
Let me know if this is what you were looking for!
I feel like that depends on a big number of factors. You need to know your business well enough to know what type of accounting software would be the best-fitted one for its needs. When I looked at the top accounting software on the market, QuickBooks was actually what best fitted my personal needs and I'm still using it to this day. I've never had any problems with it. But again, each business is different and you need to look for what's most suited for your individual needs and wishes. I'd say research is key.