When running administrative fees you have the ability to assess multiple fees on a fund.  In this situation, you can assess two fees: Then when you run the fee calculation, instead of choosing "Total" in the Method when multiple fees/fund option, choose Lowest.  See the screenshot below:

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It is also important to note that even though you have boxes indicating the minimum will be charged, as long as there is no minimum fee requirement on the admin fee charging the full fund balance, the balance will be properly chosen as the "minimum".

Making these changes to your admin fee process calculation process for this fund will insure that if the fee calculated is greater than the fund balance, the fund balance will be the amount chosen.  If the fund balance is greater than the fee, the full fee will be assessed.

Your admin fee report will show something like this for the funds with multiple codes:

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In this instance, the full fund balance of $500 was calculated for one fee and the other fee ( which was a regular 1% fee) had an outrageous $10,000 annual minimum fee which resulted in a minimum fee being calculated at $833.33.  Even though the charge the minimum fee boxes were checked, the system chose the lowest fee.  The balance fee had no minimum fee filled in so the fund balance was the lower limit.