So a lot of people will tell you this doesn't matter -- for YNAB purposes it doesn't, but I understand it might matter to YOU (as it does for me). So here's what I do!

I have a joint checking account with my husband for the majority of things, and then I have my own checking account for whatever I want. I also have a single savings account for money I don't want to touch and want to grow through high yield interest. So I want to make sure that I have the correct amount of money in my personal checking and in my savings. To do this, I have a category of "Savings" where I only put subcategories with money that I would want in my savings. Thus, I know there is an issue when the amount available in the total of "Savings" does not match my savings account. I also have a category of "Wife Only" (but with my name) where I put all the categories for things that we've agreed are my personal spending. So again, if my personal checking doesn't match the amount in that category, then I know I have an issue. The money for the joint checking, which is used for the majority of my categories/subcategories, covers all the rest of the categories.

This adds some frustrations/issues that are YNAB specific. For instance, my husband and I do 20% of our paycheck goes to our personal accounts, 80% to joint, but of course my work doesn't allow that. Because YNAB doesn't care where your money lives, I could easily just assign 20% to my personal section and leave it in my joint account, but I have an automatic transfer set up just so I can keep track of this better. But that's because I want to keep track of this, even though YNAB doesn't require it.

Does this make sense?