All you need do is change the logo's wrap format to anything other than in-line (e.g. 'in front of text') then toggle the shape's Visible property using code like:
Code:
Private Sub CheckBox1_Click()
ActiveDocument.Sections.First.Headers(wdHeaderFooterPrimary).Shapes(1).Visible = Not Me.CheckBox1.Value
End Sub
including or omitting the 'Not' according to which checkbox state the visibility is to reflect.