You can publish the two projects to different areas on your RH Server context. That way they are completely separate and have separate URLs. Perhaps if you explain a little more about why you want to have these two projects merged yet control access to different user sets we can advise more.
I did not know multiple projects could be on the same RH server without being merged. I will also assume that they can have different authoring tools. I like word and the new project most likely will use FrameMaker. Is this correct?
Yes you can have separate outputs on the RH Server BUT they all have to be WebHelp output published from within RoboHelp. Of course if you have the Adobe Technical Communication Suite you could have people authoring in Word and / or FrameMaker. You'd just need to link the relevant Word / FM files into your RH project and publish the output to the server.
Think of the RH server areas as Windows direcotries.