The ads are stored in the database.
What ad network needs you to put PHP code to display ads?
You could have your PHP in a separate file then load the PHP page in an iframe? For example, you would put
Code:
<iframe src="YOUR PHP PAGE"></iframe>
in the ad manager.
To show certain banners in certain forums you could try this:
Code:
<vb:if condition="$GLOBALS['forumid'] == XX">
<iframe src="YOUR PHP PAGE"></iframe>
<vb:elseif condition="$GLOBALS['forumid'] == YY">
<iframe src="YOUR PHP PAGE"></iframe>
<vb:else />
Everywhere else banner
</vb:if>
Change XX and YY to forumid's of where you want the banners.
To add more just keep adding elseif's... that could get messy tho.