Does the lower third template have a spot to place a logo? Like, is there a sample logo or a placeholder logo?
Most templates come with instructions for adding your logo into the template.
You could just plop your logo into the timeline, but I assume you're wanting it integrated a little better into the graphic. However, without seeing anything about the template, it's hard to know what to suggest.
I got it from freeaetemplates.com and its called Smooth Shine Free Lower Third. It doesn't have a logo placeholder. I want to add it right to the left of the text
Oh Wait I did it. I added the image to the Text Composition and it went in there. Cool!