There is a setting on a web server (i.e. DirectoryIndex on Apache 2) that determines which file is served first. If your server is setup to allow it, you can modify the order in an .htaccess file. However, be careful, because you could inadvertently change something you don't mean to when you edit config files, and editing .htaccess files that use mod_rewrite can get a bit tricky at times. ALWAYS make a backup before you try anything. For example, when I added
DirectoryIndex index.htm index.php to the top of my .htaccess file, it didn't work for me at first because there's another rule that always redirects mysite.com/index.php back to mysite.com because I don't like to see the index.php in the URL.
To answer your 2nd question, if you delete index.htm (or name it something else), then you should see index.php as a default.
I think stvwlf is right, you might consider moving the WordPress to a folder called /blog/ or something similar. It will probably cause less troubles for you. But, moving the WordPress folder takes some special care, however. Here's a guide from the WordPress documentation that should help:
Moving WordPress Within Your Site