You don't do this with an Effect but with the layout option of the clip which you put on another track.
If you already have and use two video tracks, you need to create another track which you need to place on top. With these multiple video tracks, you put your logo as image on the top clip and your "normal" video tracks below it. For your image you should take an image with transparancy like a png (or not, whatever you want). Make this logo image as long as your total video (I assume that is what you want).
Right click your logo, click properties and select layout (third tab). Try for both your begin and end clip settings something like 10%, 10%, 90%, 90% and a possible value for the transpararency if you want it to "shine trhough".
Experiment further from here.