Multisite sub folder install & Google

Hi.

I just went public with my multisite installation. This client wanted to have the blogs in subfolders, http://www.domain.com/blog1 etc.

Now that the first site is public, I can not get it indexed by google.

I created a sitemap, which I can open on browser, but in webmastertools I get: ”Network unreachable” error. From the logs I see that google is being blocked:

[Thu May 26 11:55:11 2016] [error] [client 88.xxx.xxx.xx] client denied by server configuration: /home/domain/public_html/robots.txt

The / page is still closed with a maintenance plugin. I assume, if I publish that, this error will go away.

My question is, how will Google index these blogs? They must be indexed as individual pages. Will Google show these blogs as subpages for the main domain.com? How can I make sure that that will not happend?

Thanks!