Yes, you will aggregate even if the amounts differ on different days. You take the highest balance of each account separately and add those together to determine if the form must be filed.
Then, you file as MinhT1 describes. The IRS is aware that taxpayers will regularly move money around and that this will cause these reports to not be representative of net worth. It's pretty common for folks to move the same funds around, sometimes to several accounts in a year. For example, from checking, to high yield savings, then back with additional interest, etc.
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