FIMS has the ability to associate two or more funds together to aid in fund statement consolidation and administrative fee calculation.  This feature impacts only those two areas although you can select on subordinate ( sub) funds or select on master funds in many reports.

You can set up a master/sub fund with 2 or more funds. Frequently this feature is used to consolidate an agency(FASB 136) and non agency fund together to provide a consolidated statement to the agency, but also segregate the assets for accounting purposes into the required two funds.
In the Fund module, on the Fund 2 tab, click on the Fund Statement radio button to access the location of the master/sub fund coding.

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In the example above, we have a third fund, the avian fund, that is the master to the two avian1 and avian2 funds.
It is not necessary to have a master that is its own fund.  A master can have or not have GL accounts. You could just as easily had avian1 the master and avian2 the sub fund. Clicking the Add Fund or Link to Master Fund will either add a sub fund to this one or make this one be the sub fund of another.
 
See Configuring Master / Subordinate Funds in FIMS Help Online for detailed instructions on this tab

Once linked, to consolidate fund statements you would set the option appropriately to either consolidate, show all the pieces, or both.:

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In admin fees, this option would be set to allow for proration.  As set below, the fee functions normally even though some funds have master/sub fund components.

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FIMS Online help says:
  1. Click the arrow in the Master Fund Fee Calculation drop-down box and select one of the following:
  • Not Master / Sub Basis: Indicates that the fee is not applied to Master and Sub-Funds and it is not necessary to prorate fees to multiple funds.
  • Prorate Fees Back to Funds: Indicates that you want to prorate the fees back to the funds based on each fund’s percentage of the aggregated total. Note that you can enter a percentage over 100 percent if you need to record an increase in the amount.