Also, I can't seem to find a way to enter holiday hours rather than days. How does 12pay know how many hours make up a working day?
You enter them by paying the employee using the Holiday Hours payment. Once you've got a variable hours employee thinking about holiday in days doesn't make so much sense. Just make sure that you pay them the holiday pay and they take a broadly equivalent number of days off. BUT...
At the moment, the part time employee has 14 days entitlement (she works 2.5 days (20 hours) a week and 28*2.5/5 = 14). From next month she will be working 80% every other week, and 100% for the weeks in between. What shall I do? Do I simply work out the total number of days that she will be working per year as a percentage of the full working year and change the full allowance accordingly? Or is there something that I'm missing in 12pay?
This might be the better approach in your situation. Forget about the whole holiday hours and accrual thing in the software, which really is structured much more for very casual variable-hours worked by workers in (for example) the catering or cleaning industries, and forget about the annual hours summary report. Just enter the number of paid holidays that are included in the employees salary as their annual entitlement (agree the total number of days the employee can take with them, based on the days in the old working pattern and in the days in the new working pattern pro-rata'd through the holiday year), and record them as absences when they're taken, just like any other staff member.