1. ClearCase Server is not in the standard Rational Suite package and you have to get a license separately. If you found it expensive there is another one called ClearCase LT a little bit less-expensive

2. The relation  now:

ClearQuest is a trouble ticketing application. Once a problem is found, it will be recorded in ClearQuest (CQ). An engineer will then take responsibility of resolving that recorded fault.

ClearCase (CC) is then used to take a snap-shop of the code and once the code is fixed, you check in the code back in and then set the opened ticket in CQ to a resolved state. CQ ticket can not be changed to resolved unless you modify the code or close the opened snap-shot of the code.

CC is the tool for source code version controlling a CVS. This is a much more advanced tool in comparison to Microsoft SourceSafe

CC is the one that you should use to large teams and it allows multiple engineers to work  on a single file of the same version at the same time.

It can also be used for documents too, but it doesn't show the difference of the documents of the same version and that is up to the document editor. Although it will be merged with Microsoft tools very good.