I have some games made on Scratch.mit.edu but there is no file or something to upload so how do I enter my submission?

There are different possibilities to add a scratch game. One is to download your Scratch Game and then convert it to an SWF using Junebeetle's Online Converter. I usually use the settings "Autostart" and the double resolution, that is 960 x 720. Then you get an SWF file which you can upload on the itch.io game page.
Another possibility is to make a file with html code to directly display the game via the Scratch Webpage. This article describes this, but the explanation is in German language, sorry. The screenshots and html code snipped can be helpful nevertheless, I think.

There is now a tutorial on how to Publisch Scratch Projects on itch.io.

Once you have the SWF file, how do you upload that to Itch? Itch only supports and index.html for browser games, and I don't know how to embed SWF in HTML :/

You can upload the SWF directly, to enable this, your game page must be set to type "flash game".

I did that but didnt work for me

ok, another possibility is to zip the swf together with a file named "index.html" that contains the following line: <embed src="YOURSWFFILE.swf" width="960" height="720" ></embed> and then upload it as a html game. The width and height should match what you used in the Scratch converter.