Write "Restricted funds - see attachment" on a check. On the attachment list check details and a restriction such as "Direct expenses for <blahblahblah> only." If you just do not want it to go to G&A fluff fund the execs use to live a large life, just exclude G&A: "<blah blah blah> purposes only. No G&A"

Regulations for non-profits aren't a joke. If they took your restricted funds, you bet they are going to follow the restrictions.

Non-profits may hate it but at the end it is money. So they take it. If they decline to cash the check, no skin off your back.

Source: lived in a non-profit land as a tech consultant. Heard constant bitching about big donors being smart and always restricting funds above a few hundred dollars. Execs of every non-profit that pretends it cannot deal with restrictions are taking the donor for suckers and are fleecing them.