Thomas,
I’m not clear why you would need MyEclipse to move/copy the JSP files anywhere. As you are developing, create them in the WEB-INF/jsp directory and when you deploy they will stay there, everything works fine. Keep in mind that when MyEclipse deploys your webapplication, it is basically taking everything recursively under your WebRoot directory and either creating a WAR with it, or copying it directly to your application server. So however you want your app to look when deployed, just develop like that. I suggest the following hierarchy as an example to get what you want:
Project Root
+ /src <-- Java source files, actions, forms, beans, etc.
+ /doc <-- All documentation
+ README
+ LICENSE
+ /api <-- Generated Javadoc
+ /webroot <-- your webapp is deployed from this point
+ index.jsp
+ /WEB-INF
+ struts-html.tld
+ struts-bean.tld
+ ...
+ /classes <-- Build output path
+ /jsp <-- All JSPs except for the entry one go here
+ login.jsp
+ logout.jsp
+ profile.jsp
+ register.jsp
+ ...
+ /lib <-- All libs for app
+ struts.jar
+ ...
Now when you deploy, you’re all set.