Sending Files (Uploading)
First, choose the machine you want to connect to - if the machine is not in the list, add it with the New menu.

When you have highlighted the machine you want, press Scp

Now, choose the files you want to send - you can add an entire file folder with Add File/Folder, or even add an entire set of nested directories if you click the Copy Contents of Nested Folders checkbox.

Receiving Files (Downloading)
Receiving files is only slightly trickier - you need to know the name of the file or folder you want. Be sure to choose where you want the files to go!

Here, I have chosen a file to upload. I am letting Internet Config determine what kind of file it is, and I am placing it in my web server's page root. I press Start Copy

I am prompted for my username and password. If this is my very first time connecting, I may be asked whether I want to accept the remote server's public key (used to encrypt the data); I say yes.

That's it! You will see a progress meter showing you your file being uploaded.