Steve

To remove try:

remove_action( ‘woocommerce_after_main_content’, ‘woocommerce_catalog_ordering’, 20 );
Or
remove_action(‘woocommerce_after_shop_loop’, ‘woocommerce_catalog_ordering’, 20 );

(if the above fail open the woocommerce hooks file search for the catalog_ordering and find out were its been added, then copy the line where its been added to your functions.php and change add_action to remove_action – I think)

You can align it by adding custom hooks I think and then apply css to the hooks, like in the link above. I can’t remember how I did this so Ill have to wait until after work and view my code and confirm.

Hi Calum,

Is it necessary for you to have two installs of wordpress? Could you not do something like create a /blog page and set this to show your posts? I think this could work. So your blog posts would look like:
http://www.yoursite.com/blog/post-name

I haven’t come across a scenario like yours before.
I would try the script suggested here

http://www.netregistry.com.au/support/articles/wordpress-seo-friendly-permalinks#subdirectory

and look under the “Zeus rewrite for when WordPress is installed in subdirectory“

I would remove any other scripts from both the main directory and the sub directory and place this new script in your sub directory to see if your subdirectory links work first.
If this works check your root directory links to see if they follow the script. If the main root links don’t work, I would try adding the other script file to the root directory to see if that fixes things. (so one script in the root and one in the sub)

Its a bit trail and error but its all I can think of at the moment.

again before I would go any further I would make sure that I definitely need 2 installs of wordpress.
I think things would be a lot handier if you had just the one.

Ok so I now know that to do what I am trying to achieve I need to use hooks
http://www.woothemes.com/woocommerce-docs/codex/third-party-custom-theme-compatibility/#section-1

I also edited some code to help me move the breadcrumbs to were I wanted to put them:

remove_action( 'woocommerce_before_main_content', 'woocommerce_breadcrumb', 20 );
add_action('woocommerce_before_shop_loop', 'woocommerce_breadcrumb', 20 );

But I can’t figure out how to edit the position of the sort products by drop down menu.
I have tried:

remove_action( 'woocommerce_after_shop_loop_products', 'woocommerce_ordering', 20 );
remove_action( 'woocommerce_after_shop_loop_products', 'woocommerce_ordering', 10 );

and a few other hooks but no joy removing it

I seem to have fixed my problem.

Firstly I removed the test site directory (/wp).
Secondly made a txt file on my desktop called rewrite.script.txt and pasted the code from: http://www.adamchristie.co.uk/wordpress/seo-friendly-wordpress-urls-on-namesco-zeus-servers/

into it, and put it in the root folder of my site. (in my case the Web folder)
I then copied my custom theme to my desktop and deleted it from my web folder.
Then renamed the rewrite.script.txt in my web folder to just rewrite.script, re-uploaded my theme and what do you know, no more index.php!!

I have no idea why but when I made the rewrite.script file on my desktop using dreamweaver and uploaded it, it wouldn’t work. But making a rewrite.script.txt uploading it and renaming it to rewrite.script worked like a treat!

I’m not sure which of the above steps solved my issue or if it was a combination of all of them.

Anyway hope this helps anyone else who has this problem.

Turns out instead of listing pages and sub pages it was easier to create a new menu in order to achieve what I was trying to get.

I used the code here to make the second menu:

http://wordpress.org/support/topic/on-adding-second-menu-to-twenty-eleven?replies=4

I had a problem with the ‘home’ page appearing in the second menu so I used the function found here to remove it:

http://wordpress.org/support/topic/remove-home-from-menu-1?replies=9