moving codeigniter

[eluser]Unknown[/eluser]
apologies for posting without looking to much for an answer, but I'm in a rush.

I have CI installed to root: www.mydomain.com (And everything works fine). what is the best way of moving the install to www.mydomain.com/to_here.

I copied ALL the files to the "to_here" directory and updated the "base_url" etc so the the index.php loads fine (within "to_here") and all the links say:
www.mydomain.com/to_here/my_link, but when I click a click it always goes back to the www.mydomain.com/default (redirects as it doesnt recognise www.mydomain.com/to_here/my_link).

I have .htaccess set to remove index.php which might be causing issues.

I'm a bit of a newbie, so any help would be great!!

thanks

Gee