1. Place your entire project with it's pithy name directly within your html folder. 
    Yes!
A student developer working on a website for the campus geology society might give me the following URL.

<a href="http://hive.sewanee.edu/doejj01/SewaneeRocks"> Sewanee Rocks! </a>

    But NOT NOT NOT!
<a href="http://hive.sewanee.edu/doejj01/CS284/MyProject/Final3/finalExam.php"> CS 284 - Final Project </a>
  2. Name your main file "index.php" or "index.html" (see above)
  3. All of the links to files within your website should be relative. 
    Yes! 
<a href="register.php"> Register </a>

    A big no-no!
<a href="http://hive.sewanee.edu/doejj01/CS284/MyProject/SNL/register.php"> Register </a>
  4. Tar up your entire folder from the parent folder command line prompt as usual.   (Instructions) 
    Heartily recommend... 
You follow the instructions for doublechecking. ( c. of instructions )
...and...
In the check folder, do you stay in the new directory when you click 
around?  If not, you have an absolute link address instead of the 
required relative ones...
Correct & try again!
  5. Take a look at any errors your site generates with "Tools->Error Console" or "Developer->Show Error Console" or ..whatever your preferred browser is using. Make sure you have eliminated avoidable CSS & HTML problems. For example, invalid rules that do not involve cross-browser redundancy.
  6. Check how your site looks in more than one browser. It doesn't have to look perfect everywhere and you can't check every one but you should make a good faith effort to get rid of the silly stuff.

Some of your peers (ghosts of the past) have encountered "issues" with each of the following. These issues are presented here so you can all benefit from their experiences.
Enjoy!

When you have a query that references more than one table you must join them correctly using relevant primary & foreign keys.
Don't forget in your styling that HTML5 considers article, header, footer, and nav to be inline elements. If you are using any of these tags, you can over-ride this behavior by adding the following style rule to your stylesheet: 
Recommended! 
article, header, footer, nav {display:block;}