Just before saving the file, create the folder that you want. Directory.CreateDirectory
will automatically create your folder and any other non existing folders in the specified path. After creating your target folder, just save the file to that location.
if (uploadedFile.ContentLength > 0) {
fileName = Path.GetFileName(uploadedFile.FileName);
string pathToSave = Server.MapPath("~/") + "/uploadedFiles/" + yourCustomFolderName;
Directory.CreateDirectory(pathToSave);
fileSavePath = pathToSave + fileName;
uploadedFile.SaveAs(fileSavePath);
uploadedCount++;
}