Putting that many new URLs on a new domain in the system may trigger a manual review. I would probably start putting 50K at a time over the course of 1-3 months.

Also best way to get those deeper URLs indexed are:

1) Setup the XML sitemap in webmaster tools.
2) Setup easy to crawl HTML sitemaps. Web pages with ~100 links per page that are easy to crawl and navigate through pagination.