When someone browses to a URL on your server, it uses the hostname from the URL to select the Web Site that will handle the request.
For this to work, MWS Web Sites need to be associated with the hostnames that they handle. You do this from the 'Server Settings' -> 'Web Sites' pane of the control panel using the 'link' icon for the relevant site. Sites without at least one hostname are not accessible from browsers.
You don't have a free choice about the hostnames you use - see Hostnames on the Managed Web Server for more information.
If you add or remove most hostnames ending '.cam.ac.uk' then the necessary changes will be made to the Domain Name System (DNS) to bring the hostname into use. However this won't happen if the name is in use for anything other than an other simple web site (technically, if the name corresponds to anything other than a CNAME record). If this is the case you need to discuss you requirements with the relevant institution IT support staff. If you don't want the DNS updated then tick the 'Special Domain name' box. 'Special' domain names are occasionally useful in advanced configurations such as putting a reverse proxy in front of your site.
As far as the DNS and the Managed Web Service are concerned the hostnames 'botolph.cam.ac.uk' and 'www.botolph.cam.ac.uk' are entirely separate. If you want your site to respond to both you must add each of them. However names like 'botolph.cam.ac.uk' are frequently already in use for things like mail services so adding them may be problematic.
A few names ending '.cam.ac.uk', in particular those ending '.eng.cam.ac.uk' and '.cl.cam.ac.uk', can't be automatically managed and you will need to ask the relevant department IT staff to make DNS updates for you. The control panel will warn you about this and tell you what to do next.
For hostnames that don't end '.cam.ac.uk' you have to arrange for the necessary DNS updates. See Routing requests to the right MWS server for more details.
Within the configuration of each Web Site, one hostname is marked as the 'main hostname'. Any requests handled by this site for hostnames other than the main one will be redirected to a corresponding URL containing the main hostname. This helps to promote one hostname as the 'official' name of the site.
All MWS Servers have one site called 'default'. Any requests arriving for hostnames not assigned to any other Web Site will be handled by the 'default' site. This site also always responds to the underlying hostname of your MWS Server, e.g. mws-12345.mws3.csx.cam.ac.uk, so you can always browse to it using the corresponding URL -- http://mws-12345.mws3.csx.cam.ac.uk/ in this case.