1. You can add them to your project in a number of different ways (User Library, External JAR, etc.) and then go to your project properties, under MyEclipse > Web and the Deployment tab, and adjust the deployment rules to exclude the type of resource you added them as.
2. You will want to use the Add External JAR button or add a User Library, not the WTP Runtime Libs.
3. Same strategy as 1
4. Not really, but you *can* change the output path they are built to to not be the default /WEB-INF/classes dir which gets deployed, instead you could deploy them to say /bin under your project root and MyEclipse will ignore them.