Many under the hood changes have been made since 5.11 which dates back to 2017. Consider trying out the latest. For licensed users upgrades are free for up to six months from purchase date. After that, VP will continue to fully function but a fee will be required in order to register the newest. Retain your old install file and registration info.
If a logo is a PNG image with transparent background, it can be overlaid above on a lower track which will appear in the transparent areas.
Here, the dice (PNG) have been superimposed over a (blank clip) gradient background. 
If the logo has a high contrast with its background, and no color within it that is the same as the background color it can be chromakeyed (green screen effect). Key out the background color and overlay the logo on a higher track.
Upload examples of your elements to a free server, such as MS OneDrive, Dropbox, Google Drive, get a shareable (public) link, copy that link and post it here. If using Google be sure to specify "anyone with link can view." Someone will suggest specifics.
Custom bins don't persist between sessions, unless a project is being reloaded. Create the time-lapse music, intro, etc. and export them. The resulting clips can then be imported into new projects.