Basically, when you type "site:mysitename.com" into google (with my sites actual name) the main (homepage, index.php) site isn't there at all. However, starting 2 days ago anything new I put on appears in minutes and ranks fairly high for the titles/keywords. I don't understand. Msn, yahoo, et al have everything indexed but google only has new things. What do I do to get my site fully on there? (including older articles)
Yes, that is possible, especially if the inner pages seem to have better content value than the main parts of sites like the homepage. Just add useful content And use some fewer keywords on homepage.
sounds like you're in the sandbox. watch the inner pages, my guess is they will drop after initially ranking high. the same thing probably happened with your homepage, it initially was high, then dropped low. that's typical sandboxing. unfortunately the only way to deal with this is to wait, or to not focus your traffic strategy on google.
The new pages are there because google changed their algorithm: http://googlesystem.blogspot.com/2008/01/google-artificially-promotes-recent-web.html