Actually, I've done some testing and found the method is actually very simple - am listing it here in case it helps anyone else.
Create the pay run
Annual leave accrues for all employees as per our settings
Apply leave taken
On the Employee - click Actions > Terminate employee - set leave date
QuickBooks calculated their leave allowance as 7.2 days pro-rata as they're not quite finishing the month; we have agreed to round this up to 7.5 days so the next steps are:
Actions > Accrue leave - add 0.3 days allowance of the right leave type
We then can see that their allowance from 1st Jan to their leaving day is calculated correctly, with the extra day they've taken being deducted from their pay.
This was definitely easier than we'd actually expected, and far easier than our old system, which is great - and probably why we assumed it would be more complicated!