how are you integrating the systems? are they totally different projects? are they physically separated and how are they going to interact? is there any clustering involved?

this is because, you might need to change the behaviour of some of your beans  to be either local or remote, and might need to have new locators to make remote connections transparent.

regarding entity  beans that are used by new system, this might require new relationships between entity beans and eventually will cause performace impacts. one important thing that you should note is that entity beans should only be used when you need to support concurrent access to shared data and not necessarily the data to be persisted. you better off supporting this by session  beans and dao. the more relationship you create between entity beans, the more beans will be loaded by the container and that obviously cosumes memory and slows your system down

this is very difficult to say and you need to explain more about what's going on in the integration and what is existing design in terms of ejb layouts and distribution.