Glitter - as zikreet says multiple accounts are fine. In fact the budget doesn't care which real world account your money is in, it just wants to know how much there is and what you plan to spend it on.
New YNAB handles credit cards in a slightly different way, I believe, to sort of ram home the message that debt is bad, which is highly annoying when you pay them off in full every month. Let's ignore that for now.
However, in your example let's say you and DH get paid £1000 respectively into your personal accounts and on the same day. When that money arrives you record it in the relevant account registers as 'income available this month' and then when you go to the budget screen it will show you have £2000 available to budget. If you transfer £500 from each personal account to a join account, you can record that as two transfers into the account register (so each account balance is now correct) but nothing has changed on the budget screen, you still have £2000 available to budget.
Then you allocate the money to budget categories, let's say £500 mortgage, £500 food, £500 household, £500 bills. Now as you spend things you record them in the right register (the account where the money is coming out of) and against the right category (so the budget knows which category to deduct money from).
So in this example, if your DH paid the mortgage and all the bills, and you paid for household and food, there'd be no need to transfer any money to a current account because the money is all accounted for in the accounts where it originally landed. In the real world you might want to continue to use the joint account as a way of having access to the right amount of money according to what the budget needs that month.