how do you bypass .htaccess?

[eluser]Unknown[/eluser]
i've set codeigniter to do: domainname.com/home instead of domainname.com/index.php?var=home by editing .htaccess.

i now have magento folder, so whenever i do: domainname.com/magento, .htaccess tries to use codeigniter's "index.php" to process "magento" and results in error. i just want to install magento separate from codeigniter.

How do I bypass this and still be able to use codeigniter?