Hi Tim,
The FCKeditor upload is its own thing and can't be leveraged easily for other purposes. You can make an upload using NeatUpload, it doesn't work in Medium Trust but if commented out in Web.config it degrades gracefully to built in ASP.NET upload functionality. You can study example code using NeatUpload in the SharedFiles module or Admin/FileManager.aspx or in the WebStore feature where I use it for product uploads.
Hope it helps,
Joe