The fairest way would be for all income to go in the joint pot and all joint expenses, essential and agreed joint discretionary, eg holidays, family days out etc to come from the joint pot, plus savings for joint costs like Christmas, insurance, white goods replacement etc.
After all that, split what is left 50/50 so you both have equal personal spending money.
As for the debt, is this because he's been short of personal money compared to you in the past because of the percentages system, or has he been spending more than is affordable?
If he spends £300 pm but you can only afford £100 each in personal money, it's fair that he should pay the debt back out of his own money.
But if you've had £500 pm personal money (after what you spend on holidays and other joint fun spending) and he's only had £100 pm, and he's got into debt because he's not had equal spending money, then perhaps some or all of the debt should be paid off from joint money.