First look if there is already a eclipse plugin providing this library. For apache commons you will find one. Use the plugin editor and add depencies for the desired libraries, if they are common like apache commons ;)
Other wise add directory call it "libs" and add your jars there. Then put them over the plugin editor to your classpath. To do this, use the tab "Runtime" and use the add button in the "classpath" section.
this will end up in a build.properties like this
source.. = src/
output.. = bin/
bin.includes = META-INF/,\
lib/commons-csv.jar,\
lib/commons-lang-2.6.jar,\
lib/commons-io-2.0.1.jar
Libraries which are added this way, will be exported to your plugin to and they will remain in your classpath.
The classpath of your project will be updated automaticly.
Best practice for important libraries like a DB-Driver, put them in an extra plugin project, which is not extending the UI. Plugins like this will only have a build.properties. Then you can use this library plugin as dependency for other plugins.