The best approach to ensuring that your multiple business bank accounts are well-insured by the FDIC is to open accounts with different banks and maintain a deposit of not more than $250,000 each. Another effective approach is to have different categories of accounts, e.g., partnership business accounts and single accounts under the same bank, to ensure separate FDIC cover.
We recommend up to three bank accounts and certainly two for any company that has operating capital concerns. It's important to choose banks that are very different from each other. Here is an example. There are very good reasons to do business with a local credit union, particularly if there is a regional or local component to your market. What's important is to have the second account be very different from a local credit union, most likely one of the big four or something with very different depositor characteristics. If you go with a third account, take the same approach, and make sure it's different from the first two.
One tip I would highly recommend is to consider spreading your business banking accounts across different banks. By doing this, each account will be insured up to $250,000 per bank, which can add up quickly if you have multiple accounts. It may require a little extra effort on your end to keep track of everything, but it's definitely worth it for the added peace of mind knowing your funds are fully protected.