Copying before uploading?

Hello, I am trying to find a decent webdav program and this one seems to work well. However I am trying to upload 2000+ files to a server and it is showing a windows that says copying and is painfully slow at around 300KB.
When click cancel and press the arrow (play button) in the transfer queue it starts to upload. Then I see the transfer speed of 5MB to the server.
Can you tell me what is going on? I have never used webdav only ftp so this is unusual behavior to me. Can the upload be directly to the server and skip this step? Maybe I just don't understand the process.

Also I noticed a bar on the bottom that is counting down that says Items: but is showing 4000+ and I am only uploading 2,588 items.

Try to upload a folder and not a collection of files. Then you will see a file exist dialog, select "Synchronize using Automatic Rules" at the bottom (last option) and check [x] Do this for all conflicts.

I just need to upload the folder to the root overriding the current one? So it would act like the Windows environment and say the folder exists and then ask for files overrites too?
Thank you

Not exactly but try the instructions from my last reply.

It still seems to be doing some copy dialog. I am selecting a folder on the right and then with the directory on the server that contains the same folder (name) clicking the blue arrow to transfer the folder. Is this correct or is there some other method that I should be using?
Can you explain what this whole copying step is? Maybe I just don't understand why it is doing this before it can transfer. Where are these files being copied to?

Yes this correct, then select Synchronize using Automatic Rules in the dialog.

Can you please explain the copy function?
Where is this copying to? Is it actually moving these files to a different location on my computer? If so where can I set this?