How to Go Beyond iWeb, But Not Too Far Beyond...

Hi Everyone,
I'm a big fan of iWeb, and it's really been such a great tool to help me create http://www.armansworld.com/my site. It works seamlessly with MobileMe and my personal domain, and honestly makes life so much better. I don't know advanced web design, CSS, and whatnot, plus having an automated blog and everything is great. Without it, there's no way I could produce such a site like I have now.
However, I am learning how to make my own HTML customizations, adding Javascript and other features and such to my site. But that causes clashes with iWeb.
For example, I was able to create a http://m.armansworld.com/mobile version of my website optimized for iPhone and iPod Touch. I did some research on the web and found a script that would automatically detect mobile browsers and redirect them to my mobile site. The script is great and it works. The trouble is implementing it.
iWeb doesn't help at all when you want to put custom HTML into the page—not "embedding" something, but BUILDING it in. So I open up the index.html with Dashcode and put in the additional code, which works fine. That is, until I make a change to my site and iWeb totally overrides my code, so I have to go in and put it again. Every single time. Not cool.
Which leads to another pet peave of mine about iWeb. The thing I hate the most is the fact that by default iWeb sets up the index files so that www.yourdomain.com redirects to www.yourdomain.com/yoursitename which redirects to www.yourdomain.com/yoursitename/yourfirstpage. Why don't I like it? It's because that causes my site to be bookmarked as the whole long link. Which is alright, except what if I change something? What if I change the site name, or I change the Welcome page? If I change anything then when someone tries to use the bookmark they'll get a "Page Not Found" message. I don't want that!
If iWeb could be normal and have your first page actually be located at www.yourdomain.com/index.html, that would be wonderful. I'd be much happier anyway.
So I confess: my site index.html is totally my work. It's simply a "window", a frame into my site—the link at the top never changes, it always shows www.armansworld.com. Of course I give up easy access to unique links for viewers, but I avoid trouble with future changes vs. bookmarks. So every time I update my site, I have to go in and re-do the index.html file.
Point being, I'm going beyond the entire "visual thing" and starting to want to implement my own code into webpages, however I can't do that without iWeb overriding my work. On the other hand, I'm not skilled enough to maintain the site myself without the help of iWeb. What I'd love is a compromise—a plug-in or something for iWeb that allows you to make custom code additions to any part of the page, which iWeb will totally leave alone, so you can continue to use iWeb for the site yet also make your own modifications. Modifications beyond iWeb and it's ability.
Sorry for the rant—but does anyone know of anything or have any ideas? I'd really appreciate your thoughts on this. Thanks.

Unfortunately, that is the way iWeb is and has been since iWeb 06. I assume that you are publishing directly to MobileMe when you do?
If you want to make 'custom' changes and add your own code, then when you do this, you cannot publish directly to MMe - to stop these changes being overridden, as you have found when publishing directly, go to iWeb and select the publish to a local folder option rather than ftp to MMe. Your site will then be published to your desktop.
Next download a copy of Cyberduck which is a dedicated ftp program and use this to upload your site to MMe - you need to select the webdav option to do this though as you are uploading to MMe.
If you upload your site in this way, then the changes that you implement by using html in a snippet or otherwise will not be overridden - this is how most people implement stats when using iWebSEO - they publish to a folder on the desktop from iWeb, use iWebSEO and then use this to upload their site.
This is the way you have to do it with iWeb - if you want to customise it then you can't upload directly, as you have found your site gets overridden.

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