How can I allocate one payment that has come through on the bank feed from one company but has to go to different customers(main company has 3 small totally separate)

You can do this by selecting 'find match' when clicking on the transaction - this should bring up a list of all open invoices within a specific date range (you can change this if the invoices fall outside of this). You can then tick all invoices that apply to the payment.

Thanks,

Talia