The £1000 property allowance can be claimed when you come to complete your tax return. The property allowance is a tax exemption of up to £1,000 a year for individuals with income from land or property. However if your expenses are more than £1000 it would be more beneficial to not claim the property allowance and just claim your expenses.
You can claim either the £1000 property allowance or your actual expenses, whichever is more beneficial to you. Both properties will be classed as one property business. For the joint property each owner can have the £1000 property allowance, but as stated it is either the allowance or the actual expenses.