Customer paid an invoice by bank transfer but paid in three separate payments. The payments show up in my bank register and have been reconciled invoice shows as unpaid.

Thanks Jim1954, please select 'receive payment' on the invoice and the unapplied deposit payments should then show under 'credits', where you can tick to apply to the invoice payments. If the total amount of the transactions in the bank feed is the same, you can then exclude these (tick the check box to the left of the transaction in the for review tab > exclude).