The choice is yours. There is no right way. If your application is
self-contained, i.e. it stands on its own as an application in the same
way Word or Excel does, you can choose to package it as an RCP app. If
it might need some aspects of the IDE such as an editor, you could
include the editor as part of your RCP app, or package it as a plugin.
If you feel the IDE as a whole is a useful adjunct to your code, you
can just do it as plugin. If you decide on one, and change your mind,
you can switch to the other without throwing away more than a tiny
amount of scaffolding.