there should never be an instance where the file is included more than once. to use include_once is really lazy. instead try mapping out your application in an XML editor or notepad by using tabs
mysite
[INDENT]section1[/INDENT]
[INDENT][INDENT]function2[/INDENT][/INDENT]
[INDENT][INDENT]function3[/INDENT][/INDENT]
[INDENT]section2[/INDENT]
[INDENT][INDENT]function5[/INDENT][/INDENT]
[INDENT]section3[/INDENT]
[INDENT][INDENT]function1[/INDENT][/INDENT]
[INDENT][INDENT]function4[/INDENT][/INDENT]
[INDENT][INDENT]function6[/INDENT][/INDENT]
[INDENT][INDENT]function8[/INDENT][/INDENT]
This will also make the coding of your site a lot easier