Can Coda 2 be made to uploads to locations other than the root of a website? I am using Coda 2 coming from Dreamweaver, and it all seems great.

However, uploading a file or 'publishing' (what's actually the difference here?) seems to stick the file in the root. Even when the local file structure maps directly to the remote structure. VERY annoying!

My local root is my local folder and my remote folder is the standard / web root. They should reflect one another perfectly, but uploading always goes to root.

Even if I 'drag' a file from the local view into the correct folder on the remote...it puts it in the root of the website.

The only way I can get it in the right place is to move it on the remote server and over-write it. Too long of a process to be productive as changes occur all the time in development.

Can anyone tell me how I can fix this issue? Is it a setting somewhere? I do not have this problem with Dreamweaver.
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.