Huh? So you have BoI account and BoI mortgage but you can't transfer funds? Did you actually call Banking365 because you need to do this to set it up? Did somebody in the branch tell you its not possible or was it banking365? Did you click on the button that says "register a mortage"?
I am in exactly the same position - BOI current account and BOI mortgage. The terms of the mortgage allow additional payments to be made and offset against the capital. Towards the end of last year I wanted to set up a facility such as that you describe. I was told explicitly by Banking365 that it is not allowed. You can't do it online either. And yes, I also have my mortgage registered so that the balance is visible from my current account.
Previously I asked the bank manager who set up our mortgage to send me a fax indemnity form which I could fill out and which would subsequently allow me to fax them instructions saying "Pay X from my current account against the capital part of my mortgage". The form didn't arrive. I phoned about it a second time. It still never arrived.
It looks like it might be a 'best practice' from the bank's point of view, to maximise the amount of interest borrowers pay.