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Since the institution is only acting as an agent, any receipts and letters
should come from the non-profit regardless of who sends them, and should
include the non-profit's tax id number.
The institution would accept the money in an "Agency" account, where it is acting as the fiscal agent of the non-profit.
There should be a written agreement between the institution and the non-profit regarding what each will provide and what each is responsible for.
You may also need to be careful if there are any reciprocal board or management agreements in place regarding how funds are distributed from accounts so it is clear that the institution is only acting as an agent. For example, with some institutions and state/provincial law, this type of arrangement may be best handled through a foundation rather than directly by the institution which may have legislative restrictions on these types of distributions.