WordPress Integration

I have integrated my php site with wordpress in the following way.

i have installed wordpress in the path mysite.com/blog and i use the mysite.com/blog.php page to pull the wordpress content by using the include() wp-blog-header.php code snippet and the “loop” in the news section of the blog.php .
I have set the ‘use_wp_theme’ to “false” bcoz i want to use my main site template styling for my page.
Now I have the following queries-

1.- Whenever someone clicks on the post title in the mysite.com/blog.php page it follows the permalink and the post is displayed like- mysite.com/blog/”permalink”(the wp install dir) along with the default wordpress theme.
what i want is it to show just the specific post say in a page like mysite.com/post.php which uses my default site theme.

2.- Also where can i edit the styling of the comments page for eg. the post comment button, the way in which the comments are displayed etc.

Sorry for the long post but i hope someone can answer my queries.