I'm a huge YNAB fan. Luckily it's quite easy to accurately track your mortgage in YNAB.
What I like to do is to create a "Tracking" off-budget account for the mortgage. Simply click the "Add Account" in the bottom left and choose Unlinked (you can link later). Account type will be liability. Nickname is up to you and then enter the current balance.
Then, whenever I make a mortgage payment I just transfer money in YNAB to that account and assign the transaction my "Mortgage" category. But you may notice if you ONLY do this then the mortgage balance will be lower than the actual balance due to interest accruing in the account.
All you need to do then is each time you make a payment, you also need to go into the Mortgage account in YNAB and add an Outflow with the Payee being "Mortgage Interest". You can get the interest amount to enter by logging into your mortgage website or simply take your account balance on the bill, multiply it by your APR, and then divide by 12.
See this how to calculate your mortgage amortization via a Google Sheet here.
Then, if done correctly, you should see all the numbers match up and the balance should match what's on your bank's ledger.
Another quick way to do it is also to hit the little pencil icon next to the account...
Then enter Today's Balance in the edit field. It'll then do a manual adjustment in your Register to make it match the balance with your bank. But that's a quick and dirty way. I prefer to enter the interest manually it make it match.
You can also, if you choose, track your home's value with these YNAB tracking accounts and create an "Asset" Tracking account.
Then you can update it's balance from time to time with whatever ridiculous amount Zillow says that it's worth.