/index.php how-to question

What's the best way to customize /index.php display differently than /yacs/index.php

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I see that the top level index.php is coded to look for /index.php was well as /yacs/index.php. What I would like to achieve is for /index.php to display the cover article and a gadget, while /yacs/index.php displays an article listing (slashdot flavor, probably.)

I tried an experiment/hack with something like

cd yacs
cp index.php ..
vi ../index.php
# edit code logic in index.php to always show cover article

But this didn't seem to work...I got the same markup generated at / and /yacs.

What is a good way to create a different page at / ?

Thanks,

Rod