These two get mixed up, but they do different jobs. An invoicing app helps you create invoices, send them and follow up payment. Accounting software keeps your books: bank transactions, reconciliation, reports and — in some products — your tax returns.
FreeAgent and Xero are accounting software with invoicing built in. FreshBooks combines invoicing with accounting features. Zoho Invoice and CrewSynk focus on invoicing and the work around it, and leave bookkeeping to something else.
Neither approach is better in general. One accounting product for everything means fewer tools. A focused invoicing tool can fit your working day more closely, with your accounting software or accountant handling the books. Plenty of freelancers use both — for example, CrewSynk for jobs and invoices, alongside FreeAgent, Xero or an accountant for the accounts.