Looks like there are two distinct questions here:
1) How to make web-embedded CDF content zoom (change magnification) with the rest of the surrounding web page
This is a feature now supported with the release of Mathematica 10, and coming soon with the new CDF Player. You can see this in action (using the Mathematica 10 plugin) at this Tumblr page:
http://arksphere.tumblr.com/
Use your standard web browser view menu zoom settings to see the top example change size with the rest of the page, whereas the older example below it will remain a static size. A CDF must be saved with version 10 to to enable this behavior, and we're in the process of making these updates to all CDFs in our product sites.
2) How to match a CDF based on Manipulate to the size specified your HTML
Interactive diagrams created with Mathematica's Manipulate function are scalable (to the degree allowed by white space within the Manipulate box) and will adjust their size to the dimensions set by the embed code. For fixed dimensions, configure your content with ImageSize or ContentSize set to an explicit value or size specification. ImageSize->Medium
will preserve Mathematica's default dimensions.
You'll find this and other details at the "Formatting Your Content for Embedding" section of the CDF website's deployment page:
http://www.wolfram.com/cdf/resources/deployment-details.html
</br>Hope this information helps, and I will make a point to check in later to see if there are more questions/concerns.