Claw back duty becomes payable from the date the property is first rented you then get the standard 30 days to pay. There is a claw-back section of the stamps branch in Dublin castle, I don't think there is a specific form for this, I have paid clawback by writing a letter setting out the date of first rental and the duty calculation. A solicitor would be better than an accountant to do this for you as in my experience accountants don't know too much about stamp duty but property solicitors deal with it on a daily basis. The duty is the amount you would have paid when purchasing if you were and investor so if it was a new property you get to deduct the vat paid before calculating the duty.
I don't think you'll be able to pay the duty separtately to your co-owner, the duty is due on the deed transferring the property to you both. If only half the duty is paid the revenue won't allocate this payment to one of the owners only. It would require a trawl through the legislation to clarify this. As it has to be paid anyway and as you are probably going to have to employ a proffessional to to it you might be as will to do it together.