Hi everyone.
I've taken over the design of a site and have run into an issue with the page designs. I'm a noob when it comes to magento. i have successfully created a functioning homepage, using the page.xml and magento CMS however when I click a link or navigate to another page it adds the /index.php to the url. I've found how to remove this but I still can't seem to make it load without. The only issue with the url/index.php is that it seems to be not pulling in one css sheet. I have added it to the page.xml, but there is still something missing.
Non index.php (Still in progress, I'm mostly concerned about the header.)
page.xml
<layout version="0.1.0">
<!--
Default layout, loads most of the pages
-->
<default translate="label" module="page">
<label>All Pages</label>
<block type="page/html" name="root" output="toHtml" template="page/3columns.phtml">
<block type="page/html_head" name="head" as="head">
<action method="addJs"><script>prototype/prototype.js</script></action>
<action method="addJs"><script>lib/ccard.js</script></action>
<action method="addJs"><script>prototype/validation.js</script></action>
<action method="addJs"><script>scriptaculous/builder.js</script></action>
<action method="addJs"><script>scriptaculous/effects.js</script></action>
<action method="addJs"><script>scriptaculous/dragdrop.js</script></action>
<action method="addJs"><script>scriptaculous/controls.js</script></action>
<action method="addJs"><script>scriptaculous/slider.js</script></action>
<action method="addJs"><script>varien/js.js</script></action>
<action method="addJs"><script>varien/form.js</script></action>
<action method="addJs"><script>mage/translate.js</script></action>
<action method="addJs"><script>mage/cookies.js</script></action>
<action method="addJs"><script>js/modernizr.js</script></action>
<action method="addJs"><script>js/webflow.js</script></action>
<block type="page/js_cookie" name="js_cookies" template="page/js/cookie.phtml"/>
<!-- Remove items which the RWD package is not dependent upon -->
<action method="removeItem"><type>skin_js</type><name>js/ie6.js</name></action>
<!-- Add vendor dependencies -->
<action method="addItem"><type>skin_js</type><name>js/lib/jquery-1.10.2.min.js</name></action>
<action method="addItem"><type>skin_js</type><name>js/lib/modernizr.custom.min.js</name></action>
<action method="addItem"><type>skin_js</type><name>js/lib/selectivizr.js</name></action>
<action method="addItem"><type>skin_js</type><name>js/lib/matchMedia.js</name></action>
<action method="addItem"><type>skin_js</type><name>js/lib/matchMedia.addListener.js</name></action>
<action method="addItem"><type>skin_js</type><name>js/lib/enquire.js</name></action>
<action method="addItem"><type>skin_js</type><name>js/app.js</name></action>
<action method="addItem"><type>skin_js</type><name>js/lib/imagesloaded.js</name></action>
<!-- <action method="addLinkRel"><rel>stylesheet</rel><href>//fonts.googleapis.com/css?family=Raleway:300,400,500,700,600</href></action> -->
<action method="addItem"><type>skin_js</type><name>js/minicart.js</name></action>
<!-- Add stylesheets with no media queries for use in IE 8 and below -->
<action method="addItem"><type>skin_css</type><name>css/styles-ie8.css</name><params/><if><![CDATA[ (lte IE 8) & (!IEMobile)]]></if></action>
<action method="addItem"><type>skin_css</type><name>css/madisonisland-ie8.css</name><params/><if><![CDATA[ (lte IE 8) & (!IEMobile)]]></if></action>
<action method="addItem"><type>skin_css</type><name>css/ccn.webflow.css</name><params/><if><![CDATA[<!--[if (gte IE 9) | (IEMobile)]><!-->]]></if></action>
<action method="addItem"><type>skin_css</type><name>css/webflow.css</name><params/><if><![CDATA[<!--[if (gte IE 9) | (IEMobile)]><!-->]]></if></action>
<action method="addItem"><type>skin_css</type><name>css/normalize.css</name><params/><if><![CDATA[<!--[if (gte IE 9) | (IEMobile)]><!-->]]></if></action>
<!-- Add stylesheets with media queries for use by modern browsers -->
<action method="addItem"><type>skin_css</type><name>css/styles.css</name><params/><if><![CDATA[<!--[if (gte IE 9) | (IEMobile)]><!-->]]></if></action>
<action method="addItem"><type>skin_css</type><name>css/madisonisland.css</name><params/><if><![CDATA[<!--[if (gte IE 9) | (IEMobile)]><!-->]]></if></action>
<action method="addItem"><type>skin_css</type><name>css/ccn.webflow.css</name><params/><if><![CDATA[<!--[if (gte IE 9) | (IEMobile)]><!-->]]></if></action>
<action method="addItem"><type>skin_css</type><name>css/webflow.css</name><params/><if><![CDATA[<!--[if (gte IE 9) | (IEMobile)]><!-->]]></if></action>
<action method="addItem"><type>skin_css</type><name>css/normalize.css</name><params/><if><![CDATA[<!--[if (gte IE 9) | (IEMobile)]><!-->]]></if></action>
<!-- Sets viewport meta tag using text block -->Thanks!