You can auto pay and still stay on top of things. We have all of our bills that allow free autopay set up to do so and those that don't we have set up on our google calendar that we check daily.
We also use YNAB to track everything and try to avoid going more than 2-3 days without updating our budget's current status.
We still write checks to some smaller organizations (Church, kid's sports, etc.) that don't have an easy way to take our cards or when we're paying friends (for instance, we're going on vacation with some families, so we wrote a check to cover our portion to a friend) and the reason I hate doing that is that you are at their mercy as far as when they cash it. Obviously, you can write it down and keep track of it like that, but I like to update YNAB and make sure the balances match what the bank is reporting.
In any event, I'd say do what works for you. At the end of the day, in my opinion financial workflows are similar to working out physically - there are any number of options and differing opinions, but for 99% of people, the best option is "the one you'll do" and if you have a system you are using and it works for you, I wouldn't worry too much.