WinSCP cannot archive a directory on a remote server.
All it can do (with some limitations), is to execute a remote shell commands.
That does not mean, we should provide support for all *nix shell commands here.

I am using the program WinSCP to archive a directory on a remote server, how is that nothing to do with WinSCP? It is a custom command of WinSCP. I am just trying to figure out how to save the folders when extracted. Is it not capable of doing this?

Well, your question has nothing to do with WinSCP. We cannot support rar command here.

I am trying to archive a directory on a remote server and have it keeps all the folders in tact. I tried using the command " rar a -ep "!?&Enter an Archive Name:?archive.rar!" !& " without the "" and it did archive everything but when I extracted the archive on my local computer it just had all the files (over 6000 files) spread out with no folders. Is there anyway I can keep all the folders that I started with and keep everything within those folders to stay there?