Can Coda 2 be made to uploads to locations other than the root of a website?
Publishing is different than uploading in Coda.
Uploading will just upload to whatever folder you are in in the web view (bottom of the file list pane, 2 icons, local and remote).

So if you are in the root on the web view pane, anything you 'upload' will go there. If you want to upload by manually 'uploading', navigate to the folder you want in the web view, then whatever you upload will go there.

If you want to upload files retaining their structure, you want to 'publish'. So you can either 'mark for publish' or when you save a file, it gets marked for publish, then you can publish the lot, which will upload everything in its right place.

Of course, this all depends on your folder settings. Make sure you have the right info in your settings pane, for local folder root and remote folder root etc.