Vlad,
Yes actually a good number of our users are moving over from previous IDEs. While most of the time only minor reorganization is needed, sometimes no reorg is needed and other times a fairly large amount of reorg is needed. Our project structure is that of an exploded WAR file. This is the most ‘standard’ format for a web application and allows us to offer some nice icing on the cake, like deployment tools for you.
A good way to get your project into MyEclipse is to load it up, create a new Web Module Project. Then you can start copying your source files into the appropriate location, moving your JSPs into the appropriate location under the WebRoot, xml files, and anything else. (don’t forget to put libs in the WEB-INF/lib dir as well).
If your project uses struts, you can add Struts Capabilities to the project (right click on the project root, go down to MyEclipse, and select “Add Struts Capabilities…”) and then do what I just mentioned to pull everything in. You can then move around whatever you need to until the project builds completely.
Let us know if you have any problems doing this, and be as specific as possible and we can help you run it down.