In the context of Servlets, it would probably be best and easiest to configure the "MySQL connectivity" in the servlet container / application server.
How that works exactly is container dependent. If you can tell us which container you are using we'll take it from there
Build a man a fire, and he'll be warm for a day. Set a man on fire, and he'll be warm for the rest of his life.
I'm going to assume Tomcat 7, but there's similar documentation available online for earlier versions.
This is the server documentation index.
What your looking for is the JDBC Datasource section. It should contain an entry on how to configure a MySQL data source that uses DBCP for connection pooling.
It might be useful to read the JNDI resources section first though.
As for using Eclipse to develop Servlets and JSP pages, you'd probably want to have a look at the Web Tools Platform. Documetation can be found here.