Your life will be much easier if your shopping cart or merchant service software can talk directly to QuickBooks Online (QBO). Shopify is my current recommendation for an entry level online shopping cart because it does work well with QBO. It can push detailed customer and sales data to QBO as well as bank deposits and merchant fees. If your service can’t talk to QBO we can figure out the best way enter summaries of your sales and fees manually. For simply accepting credit card payments, you can’t beat QBO's integrated QuickBooks Payments service for convenience.
You should decide whether to track individual customers in QBO. QBO has a limit of 10,000 names total, so if you are a volume seller you might hit that limit. You customer list will be in Shopify (or your other merchant software) and can be linked to other apps for marketing and analytics. In that case QBO will simply track your revenue and expenses for financial reporting purposes.
As of the last few months, I can now recommend QBO for inventory. Shopify can track the quantities of your items sold and sync them back to QBO, but it can’t track your purchases and costs. You can enter purchase quantities separately into Shopify (the dreaded double entry). You may want to do this, because Shopify has some nice features. You can set Shopify to warn customers that there’s only 1 or 2 left, and you can set it to disable the item if it’s sold out.
I can help with the busy work of setting this all up and making sure it’s working.