Well, you need to migrate your server from 4.x to 6.x, meaning that all your 4.x settings is replicated on the 6.x server. There is some documents regarding that issue
here. Look under WAS 6 - migration guide.
Then, you would have to migrate your code. It depends on what your development environment is, but like I said, for instance you could use the migration wizard in RAD or RSA and
test it with the built in WAS 6 test environment. There is also some forums dedicated to migration over at
developerWorks. This is not a trivial task, especially if your code is very old. But you have to start somewhere and IBM's help pages is a good place to start. You will have to expect a lot of reading, searching, trial and error in order to complete such a task.