Quickbooks is not a database, it cannot handle importing every order and will eventually fail when abused.
If you don't care about this, then look into Webgility, it will certainly take care of this issue but is very costly.
If you just want to do this yourself as quickly as possible, look into Exportly, here's the link
We also have Quickbooks and if you ever find a solution that doesn't cost a monthly fortune, please share! I ended my relationship with Clover because their services were becoming more and more obsolete, yet still advertising these services were included, and basically forcing their customers to purchase 3rd party apps at an additional monthly cost to acquire the services. None of which were exactly "affordable" for a small business. When I say "affordable", as a 350 sq.ft. brick & mortar storefront, I simply could not afford to pay a POS $80-$100 a month, plus the per transaction fee and then pay an additional $20 a month just to print a barcode label, another $50 a month to track my inventory, $99 a month to sync Quickbooks, etc. And yet, most of these POS systems lack the capability to perform basic retail end of year auditing for tax preparation. I'm hoping either Shopify or another POS system who understands business operations will perhaps come up with a better and affordable solution.
Unfortunately the 3rd party apps pricing will just continue to increase as time passes and the product their selling will still be inadequate.
I would advise obtaining the services of an eCommerce Accountant, they do everything for you so you can focus on running your business instead of working in it.
They will provide weekly/monthly KPI's, financials, and inventory valuations so you'll know what product is profitable and which ones you need to stop selling, or at the very least raise the unit selling price to break even.
I gave up. I tried some import/exports and what a pain. I got a couple of quotes from ecommerce accountants and they were well out of the range of ROI.
So I hired a bookkeeper to spend a few hours a month to input into QB the absolute basic info from our Shopify sales. As long as I keep ahead of her with entering my POs and receipt for parts, it's been about $200/month. If she needs to add new parts not previously in the system, it slows her down and costs me more. As I'm using QB online and she can access my Shopify invoices, it's been pretty smooth and she can spend a few hours in an evening catching it up. Date, invoice number, product sold and verification of provincial taxes is all that's being entered. I figured we can always track back to Shopify based on the invoice number, so full customer details become unnecessary.
For my POs, I only enter them once - into QB. Using the incoming inventory function in Shopify seemed to be too much work. The only sticking point I'm finding is I then have to update quantity in Shopify because export/import is just ridiculous to format. Nothing exports out of QB that can be readily imported into Shopify without a whole lotta modifications. It's just not worth the time and effort. So I bring up the inventory screen and manually change the quantities when I get product in.
I am finding some issues with inventory using this dual system, but we only have about 3000 of our 10k+ parts in Shopify so it's been pretty quick to do spot inventories of fast moving parts. In a sense I don't care so much if QB 'lags' behind Shopify a bit - as long as everything matches up for year end. For the customers, as long as they know I have the part in stock, that's all that matters on the front end.
If anyone has other suggestions I'd be interested in hearing them. This time of year I'm entering a couple hundred new parts a month into Shopify (in part due to the pain of manually changing shipping on each part - that's another topic) but have plans to do some bigger loads in our off-season.
I'm glad you've found a system that works for you, but that is a lot of manual labor which creates keying errors, but it does give someone a job. For my clients I import everything, if that's what they want, or just the basics, and I can do about 10,000 orders in 10 minutes, once I have the client built into my system.