When I add multiple embeds to a single page in onMessage, the new embed seems to override the previous one.
At this time multiple embed codes cannot be added to a single page in onMessage. When two embed codes exist on a single page both are trying to use the same div ID (bbox-root) which is what the page uses to run the embed code. When the code on a page with multiple embeds runs, it will use the first instance of the embed it encounters since the ID's are not unique. This is why the second embed code appears to be overriding the first one.
You will need to either obtain a new, single embed code from the creator of the embed or you will need to only use one embed per page.