Your take home pay won't be 3x hers due to how tax works. Plus if you pay into a pension, she will be entitled to some child benefit, because your 'effective income' will be less than £60k, unless you also have a company car, which also affects things.
It sounds like she currently has a lot more spending money than you because she only pays for some groceries, minimal afterschool clubs and some of DCs clothing, while you pay for everything else and her income is made up of her salary, maintenance and over half the rental income for the annex - does this count as 'rent a room' or is it a self contained annex so the income is taxable?
If that was the case, it would be better for the income to be hers on paper, because there would be less tax to pay, although it's probably worth discussing this with an accountant.
Although unless you have a huge mortgage, I would have thought that you should both have a decent amount of spending money with £80k income, plus maintenance and rental income.
Seeing as you seem to be happy to contribute to the DC costs, the fairest thing to do would be to pool all your incomes (salaries, rental income, any CB, maintenance) and pay all joint costs including mortgage, bills, groceries, car costs, DC costs, house maintenance, savings for annual and irregular expenses like insurance, holidays, appliance maintenance etc out of that and then split the remaining 50/50 as personal spending money, but I suspect that she wouldn't like that as she would end up with less money.
You say you don't know what she spends money on - does she have expensive hobbies, spend a lot on grooming, clothes etc, always decorating the house, buying new furnishings, spends a lot on food, always eating lunch out or travelling by taxi, or could she have a lot of savings that you don't know about? Do you both have decent pensions?