It looks to me that you are trying to do a bit too much work for what you are trying to accomplish.
It sounds like you just need one WordPress installation, and two parent categories.
I would install WP in a directory such as http://example.com/wordpress – and set the blog URL to http://example.com – I believe this is what you did for the original /blogs/ installation.
From there, create two main categories, blog and articles. In the WordPress settings, under Permalinks, set a custom permalink structure of /%category%/%postname%/
This will cause any posts in the blog category to have the URL of http://example.com/blog/postname and any post assigned to the category articles to have the URL structure of http://example.com/articles/postname
These articles should help:
http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory
http://codex.wordpress.org/Using_Permalinks
That def make more sense. So in regards to the PHP code i posted. My example.com isn’t a wordpress page at all, its just my sites homepage with menus and images etc, so what code would i need to post the recent posts from each of blogs/articles?
Thanks
Ok, sorry, I didn’t realize that the root already had a site built on it, I was assuming a fresh setup.
I’m unsure if my earlier advice would be the best in this case then. If the original page can be converted to a WordPress template page (you can set a static page as the homepage in the Settings -> Reading panel) that would make this a bit easier, otherwise I am unsure about having the two categories located at /blog/ and /articles/ respectively without causing an issue with your current homepage.
If you can integrate the pages currently located in the site root with WordPress, then to show a single post from multiple categories, I would try something like this:
<?php //store original query ?>
<?php $temp_query = $wp_query; ?>
<?php // Display one item from 'blog' category ?>
<?php query_posts('category_name=blog&posts_per_page=1'); ?>
<?php while (have_posts()) : the_post(); ?>
<h3> <a href="<?php the_permalink(); ?>"><?php the_title(); ?></a></h3>
<?php the_excerpt(); ?>
<?php endwhile; ?>
<?php // Display one item from 'articles' category ?>
<?php query_posts('category_name=articles&posts_per_page=1'); ?>
<?php while (have_posts()) : the_post(); ?>
<h3> <a href="<?php the_permalink(); ?>"><?php the_title(); ?></a></h3>
<?php the_excerpt(); ?>
<?php endwhile; ?>
<?php // replace original query ?>
<?php $wp_query = $temp_query; ?>
This should display 1 post from each of these categories, the code is modified from an example found here: http://codex.wordpress.org/The_Loop#Multiple_Loops_Example_2
