It should create a mesh, otherwise there is nothing to render! 
But it won’t let you export it, so I can understand that you missed that.
About your alignment problem I can only say that there are plenty of threads here dealing with similar problems, so I suggest you check out those first. I would start in FAQ https://support.capturingreality.com/hc/en-us/articles/115001485012-How-to-put-together-more-components-
If you then still have issues, then people here might further help you. Screenshots help enormously. But since this is a thread about the box issue, you might want to open your own or join inwith a more specific one.
If it helps anything, I think everybody goes through the initial problem with too many components…