Well, in the html file you should only add the upload form, unless you want "all-in-one"... Then you should put all code in one php file.
The form could look something like this:
<html>
<head>
<title>Upload</title>
</head>
<body>
<form action="upload.php" method="post" enctype="multipart/form-data">
<input type="file" name="upload">
<p>
<input type="submit" value="Upload Files">
</form>
</body>
</html>
