Magento Magento Testing With Centmin

So far so good i got a store up and running with a few tweaks i will post the config for anyone looking and it does run very well. So as soon as i have it all sorted out with ssl and all that i will break it all down.

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I am having difficulty with only 2 things it seems magento system generated url rewrites or seo urls work out of the box but any custom urls no matter what code snippets I use will not rewrite without index.php. I will post the configuration if anyone has any suggestions.
ex. Magento system writes urls like so
example.com/category/product
if you have a custom page like so
example.com/foo.html it adds index.php
no matter what I have tried.The problem is with heavily modified template structures there are a lot of custom urls. Having trouble also with getting a go daddy ucc ssl cert working. So that's the update for now. I will try to post con figs if I do or do not figure it out.