normally after you edit you index.php, just copy the htm code in the index.php file.
few options.
1. edit your index.php on file manager
2. usually the htm code will be placed on the body or header, say your index.php contains
Code:
<body>
...your banner code here
...
...
</body>
3. your htm code should look like,
Code:
<a href="the affiliate link"><img src="the image location sometimes residing on affiliate site"></a>
4. save the file and you are ready to go.
I am willing to help you if you want to place the code here