I don't think your problem is as complex as you think. You have two sites right, a marketing site and an application. If it is just this I would keep both site

I don't think your problem is as complex as you think. You have two sites right, a marketing site and an application. If it is just this I would keep both sites under the same domain and deploy your application to a sensible sub-directory. Alternatively you can make a sub-domain for the app, but this is just slightly more work since you will have to take care of this in your DNS settings. However, if you are planning on giving your users each sub-domains then you are talking about something way more involved. Clarify your question, and I think you will get better help.