You can use this method to add a new error to an existing validation summary control from your code-behind page.  Don't forget to use the proper ValidationGroup that your validation summary is using.
protected void AddErrorToValidationSummary(string errorMessage)
{
    CustomValidator custVal = new CustomValidator();
    custVal.IsValid = false;
    custVal.ErrorMessage = errorMessage;
    custVal.EnableClientScript = false;
    custVal.Display = ValidatorDisplay.None;
    custVal.ValidationGroup = "MyValidationGroup";
    this.Page.Form.Controls.Add(custVal);
}