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non-www, www and blog subdomain: Advice sought regarding

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Hi.
I hope I have this in the right section.

I have a domain that has been used as an online store for my small business. I used to use self-hosted wordpress with an ecommerce plugin.

The preferred domain set with Google was the non-www version.

Now, I just transferred my shop to an ecomemrce provider (Indiemade, it's like shopify). They insisted that I must CNAME my www version to their site.
So that's what I did. I set up the CNAME and then changed the preferred version in Google WMT to be the www version.

Now, I have set up a sub-domain for my blog (blog.)

Thing is, I'm sure I have left something out. I have a bad feeling that there's something I should be doing that I'm not. I feel a bit confused about what is going on. Where does my data show in WMT? I have registered the blog subdomain on WMT, submitted a sitemap and fetched, but after more than a week no pages are indexed.
The www version in WMT is showing indexed pages, but only 10. Not nearly enough. The non-www shows 77 are indexed.
Doing a site: search on Google brings up the blog pages, and mostly non-www pages of the main site, all of which show a page not found when clicked.
Does all of my data show in my preferred domain in WMT, even the blog subdomain?

Would anyone be so kind as to offer some advice to move forwards, perhaps things I may have missed and what I should be doing to deal with the old pages that no longer exist?

Regards,

Richard.
 
the www version can be ,technically, another site, so you can register and verify it in webmaster tools. Just confirming you are in control of this other version is generally good practice although it can get a bit unwieldy if you have a multiple number of sites.
 
Have you setup 301 redirects from non-www to www?
Have you sense-checked the basics? (robots.txt, etc.)

Generally I would recommend using domain.com/blog rather than blog.domain.com. Subdomains are considered separate content and site footprint is a useful ranking factor.
 
Thanks for the replies.

I agree, it has got unwieldy...

I have a set up a 301 re-direct for the site, but not for individual pages. Should I be doing something for individual pages that are now in different locations?

I used the subdomain for the blog because the blogging platform provided by the ecommerce site wasn't what I wanted, but everything else was. Not perfect I know, but I thought I could cope with the complexities introduced.

How long should it take Google to 'figure stuff out' about the changes to the site? It's been a few weeks already...

Thanks again guys,

R.
 
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