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PHP issues -directories, Codeblocks and SimplePHP

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I can't find the next step to answering this issue and need to get this code up and running right away. Please point me to the right info if it is already answered somewhere else.

I have written php code for much of my sites functionality which imports and exports data to MySQL and some txt files. I just want to move the php over to Concrete5 for the look and feel. I've added single_pages for the top level of each of the sections. I'm having trouble figuring out the paths from my php entries to the subpages that I'm creating for the html. I've put the scripts in /scripts/ as well as single_pages/mystuff/ folders but keep getting redirects to /basedir/index.php/mystuff/page-handle instead of the single_page dir or scripts. This is the php in my single_page.
<?php
echo "Directly calls clinicians subdir" ."<br>";
echo '<A HREF="./mystuff/links_clinicians.php">Edit an existing clinician</A><br>'; //doesn't work
echo '<A HREF="./add-clinician">Add a new clinician</A>'; //This actually works
?>


Also, I can't figure out how to use Simple PHP or CodeBlocks Php blocks to move my site. I've encountered the problem with Simple PHP that was discussed before; the bottom header row gets installed into the same area. I haven't figured out to use CodeBlocks php and can't seem to find the documentation or samples anywhere.