Where you set an invoice number depends on where you are creating your invoices:
Xero
Invoice numbers are automatically assigned by Xero. When SortScape creates an invoice, Xero uses your organisation's invoice numbering settings (prefix and next number) configured in Xero. To change this setting in Xero go to Xero's Settings > Invoice Settings > Default Settings.
QuickBooks Online
If you have the “custom transaction numbers” setting enabled in QuickBooks Online, SortScape will try to "guess" the next invoice number based on the invoice number of the last invoice created in QuickBooks.
If invoices created in QuickBooks Online are not getting allocated an invoice number, then turning off the “Custom transaction numbers” setting in QuickBooks Online should fix the problem.
Note - changing this setting won't update existing invoices but will apply to any invoices you create after disabling custom transaction numbers.
Invoices within SortScape
If you are creating invoices in SortScape (i.e. not in Xero or QuickBooks Online) then you can set the invoice number when creating the invoice. Future invoice numbers will then follow that pattern

