I have created a CustomValidator control
public class MyValidator :CustomValidator, IScriptControl {}
and also created the equivalent client sc
You can set the ClientValidationFunction property of the base class like this -
base.ClientValidationFunction = "MyCustomJavascriptFunction";
So, it will render it like this -
MyValidator1.evaluationfunction = "MyCustomJavascriptFunction";
You can do it from the control also by setting the same property.
EDIT: You can do
document.getElementById("<%= ValidatorId %>").evaluationfunction = "MyCustomJavascriptFunction";