There is no difference. Cookies are cookies.
The only way (though highly unreliable), is to remember in the session whether you set the cookie from PHP. If not, then it might have been set from JavaScript. But like I said, this is unreliable. The cookie might have been set from PHP in an earlier session, or someone might have manually messed with the cookies.
I think the best way is to use session variables altogether. The session keeps the leading value on the server. If you need the value in JavaScript too, you can set a cookie, or add the value in a small script, but in PHP you never read back the cookie value at all, just use the session value on the server, and to reset the cookie on each request, so the client knows that value too.