Different people like to order their invoices in different ways, and FreeAgent tries to accommodate this where possible.
The simplest type of invoice numbering (and the default) is global invoicing. This means your first invoice would start at 001 (actually any number you choose) and increment by one each time: 002, 003 etc. This is the type of invoicing scheme favoured by accountants as it allows the simplest way of tracking payments.
The next level of invoice numbering is contact level, which keeps a consistent contact reference prefix at the start of the invoice number. If you had a contact "Joe Bloggs", then your contact level invoice sequence might go JB001, JB002, JB003 etc for all projects for that client. You set this level of invoice numbering on the New Contact or Edit Contact screen.
The last type of invoice number is project level sequencing, where the prefix is related to the project and not the client. So you could have BIGPROJ001, BIGPROJ002 for your different invoices for that particular project. This can be set on the New Project or Edit Project screen.
Note: the actual prefixes for Contact and Project level invoicing are added when you create the first invoice for that project, not on the Contact or Project screens.
When you view an invoice on the New Invoice or Edit Invoice screen it will tell you what invoice numbering scheme has been used for this invoice. This is where you also begin your numbering scheme by adding the desired contact/project prefix or simply adding a number if you wish to use global invoice numbering.