If I understand correctly: you want the Perl and the PHP to use the same sessions. The good news is what you are trying to do is possible. The bad news is, it won't be super easy for a beginner.
As mentioned, the cookies are in the HTTP headers (not in the HTML at all). So you won't have to put them in pages. You will have to, probably, normalize your Perl to use the PHP session. This should do that for you: PHP::Session.
This isn't hard for an experienced web dev but for a beginner, not so fun. If you can provide a small example of the Perl you need to share the PHP sessions--a working CGI--you'll likely get better help.
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