The first battle, though it's only a tussle, is deciding between a cloud accounting software or a desktop based one. With your store hosted online, it makes absolute sense to record transactions and finances on the cloud. A rapidly growing number of smart e-commerce store owners are flocking towards web based accounting solutions. 27,000+ have adopted QBO over QB Desktop due to its flexibility and accessibility. Besides, cloud has a lot of benefits over desktop, we list them here for a quick reference:

Moreover, if yours is a fast growing business working with 5-6 cloud business apps for activities like Payments, Invoicing, Marketing, Customer service etc., you cannot integrate it all with your desktop accounting software which further isolates the accounting function from your business operations