SEO for phtml and dynamic pages

Phtml pages giving me nightmares

[Rocknroll]

Hey Guys,
I am new to this webmaster community. I am currently working on optimization of a site which is all dynamic, pages are with extensions .phtml (what are these?). I am against all these problems and would appreciate any help with any of these : Here is the scenario:
The whole site is dynamic (though i checked that most of the pages are indexed by google). All the meta tags are same for each and every page! and the CSS and JavaScript for the vertical drop down menu takes first 300-500 lines of code on each page! and actual content shows after 500th line! From what i know , google reads the content as we see it by (View > Source) and just crawls first few thousand words ). The content is really relevant to the keywords i am focussing on but the site shows up nowhere on google (maybe on 10th page). The whole structure is very complex. Every page is just made by calling external files (CSS, JavaScript, even flat text files for content).
What can i do to make the pages simpler and bring the content higher up in the code?
Can i move CSS below the body tag?
I cannot move the code for drop down down coz it messes up the whole page.
Any suggestion to move my content higher up?
I would appreciate any help as i am very new to this whole dynamic site and .phtml. I have recieved very impressive results with the static sites. Please help all the genius minds here. THANK YOU.

[JohnKelly]

.phtml siginfies pages using PHP code (I've also seen .php, .php3, .php4).

I'd move all code between the HEAD tags for javascript and style sheets to their own separate files, like this:

<script language="JavaScript" type="text/javascript" src="/somedir/javascripts.js"></script>

<link rel="stylesheet" type="text/css" href="/somedir/styles.css">

Hope this helps.

[Rocknroll]

Thanks John,
This is where i get confused, I am keeping the CSS and JavaScript in external files and call them as you mentioned here. BUT when i view my source using View>source from my browser, I see all that CSS code and JS right there. Is that the way all the SE's (esp google) see or index our pages? Please clarify if I am right here. I am really greatful to you for your help. Thanks

[JohnKelly]

Sorry, I missed the part where you said you were already calling them as external files.

I'm not sure why you're still seeing the code. There are parts you're supposed to leave off when you include them in external pages. For instance:

The style.css should contain only the following bits:

{
H1 { font-size: x-large; color: red }
H2 { font-size: large; color: blue }
}

and not

<STYLE TYPE="text/css">
<!--
H1 { font-size: x-large; color: red }
H2 { font-size: large; color: blue }
-->
</STYLE>

leave out the STYLE tags and comment lines.

The Javascript external file is much the same -
use:

function whatever(var) {
code goes here
}

and not:

<script language="JavaScript" type="text/javascript">
<!--
function whatever(var) {
code goes here
}
-->
</script>

Leave out the SCRIPT tags and comment lines.