Yes, there is an undocumented way (it's ugly, but it works): if you are connected with github, you can create a file called apiary.manifest
in the root of your repository.
Inside it, you can put newline-separated list of relative paths that are concatenated in that order and shown on your apiary subdomain.
Please note, however, that apiary currently doesn't provide a good way to edit this in the apiary editor. Should you save it there, you'll just get concatenated version saved as apiary.apib
back in your repo (this is why it's undocumented).
You'll have to use your editor to edit the blueprint further, i.e. sublime with apiary plugin.