IWeb, MobileMe, google webmaster difficulties.

I've been working on a website that is designed to represent a small business I am starting.
I purchased a domain name and I use my MobileMe account to host it, I subscribed to MobileMe solely for this reason.
I have made a small site, 12 pages or so, in iWeb and uploaded it to my personal domain name.
I then subscribed to google webmasters product and subsequently it seems like I have a penalty on my domain which means that google don't index it and it is excluded from searches.
I have been told that this is something to do with the way iWeb creates sites.
My sites homepage appears like this www.mydomiain.com/Site/Home.html
I would like it to simply start at www.mydomain.com
Firstly, how do I do that?
Secondly, how should I go about making my site google friendly? I use iWeb SEO app but until I can figure out how to reverse the violation penalty that iWeb has caused iWeb SEO software is not particularly useful.
I would like to delete all unnecessary iDisk folders, all I want to use it for is hosting my domain name. Which ones can I delete?
Many thanks.

MobileMe cannot host your domain name, only your website. There is no reason to delete folders from your iDisk as it won't host your domain name.
Apple is not a domain name registrar and you can only host your website with them, not your domain name.
You purchase your domain name from a domain name registrar and they are your domain name hosts - all you do with MobileMe is link your domain name to your iWeb created site hosted on MobileMe.
You must then proceed to link your domain name to your website, so you must enter your domain name into the personal domain name settings of your MobileMe account and then you must go to your domain name registrar and log in here and set up CNAME forwarding to link your domain name to web.me.com.
You are still always publishing your site to MobileMe and never directly to your domain name, but you are simply linking the two together.
As for the site name in your url, this is normal site structure for iWeb and if you are using CNAME forwarding and publishing to MobileMe there is not really a lot that you can do about this.
As for iWebSEO, this works well and I use this for my own website, but for it to work, you do need to use it post publishing, so you would need to publish your site to a local folder and open the html files using iWebSEO and then adding what you want to and you can then use iWebSEO to upload your site or you can simply drag and drop the files to your iDisk.
There should be no problem and your site should still be found.

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