By default the invoice numbering is by date. If two invoices are generated on the same date then the invoice number will be appended with alpha. eg: 160312, 160312A, 160312B, etc..
To make the invoice number match the "Job Name" the invoice was generated from, set the advanced field "invoice_name_match_job" to 1
To make the invoice number an incrementing number, set the advanced field "invoice_incrementing" to 1, generate an invoice, then set the new advanced field "invoice_incrementing_next" to the starting invoice number you wish to use.