No, it creates its own area in the AD Configuration during installation.
You can try restarting certificate services and see if that helps.
You can also try this command ran from the CA: "certutil -vroot"
This will recreate the web pages and fixes things a decent amount of the time.
If that still doesn't take, reboot the CA server.
If you are just trying to get to the root certificate chain, the CA certificate should be stored on the CA in %systemroot%\system32\certsrv\certenroll directory. If you have multiple CA servers (e.g. root CA and subordinate CA) you should get the cert for at least the root, but sometimes it helps to get the cert for each CA.
You can right-click the cert file on the client and install certificate, follow the wizard. If the defaults don't take you can try manually selecting the store and browsing, checkmark on for 'show physical stores' and then select trusted root certification authorities.