My friend used to write a big "D" on all the checks they deposited because they deposited them through a mobile app. Also they would keep all the deposited checks in a separate place and not mix them up. They kept track of how much they should have from different places they received a check.
How can you not miss a $500 to $1,000 money order. I personally don't keep a ton of money in my checking, I keep it mostly in my savings, so I will definitely notice if I haven't deposited enough money since I would have to pull an extra $500 to $1,000 out of my savings.
You have to do these little things so you don't short yourself when dealing with thousands and thousands of dollars per month.