It is possible to have both in one system, depending on what one wants for speakers and the space one has to put it in. And it is cheaper that way, both in terms of equipment and in terms of the home to put it in (as two rooms cost more than one), so it is what most people should probably plan on doing.
I personally have a separate main two channel system and home theater system, but my home theater is far better than most people's main stereo. And I don't want a home theater in my living room, though I do want a good sound system there. So for me, having two separate systems makes sense. However, one can do it with one system, depending on what one selects for one's speakers.
So, what speakers do you have in mind for your "high-end speaker system?"
And do you want all of your audio in one room, or do you plan on having a system for a home theater in one room, and listen to music in another room as well?