This is a tricky one. It is a feature request on the
road map but there is no easy way of doing it currently.
One method which may work, but I'm yet to test, is to create two overlapping events above the main video. These events need to be less than the minimum length your video will ever be and, when combined, greater than the maximum length of your video.
Let's say your videos are roughly six minutes long but never shorter than five minutes. Create two five minute events with your logo. One event lines up with the start of the template. The second event lines up with the end of your template. As the video is created and the length changes to accommodate the source media, these two events will slide past each other to effectively cover the whole video.
I'll do a quick test and see if I can get it working.