A year or so ago, I read an article that gave a list of DM Tips that could help your game run more smooth. In that article it mentioned that there always seemed to be an awkward break in action to start combat and have everyone roll initiative. The remedy to this seemed simple, have players roll initiative right before you start playing for the day. By doing this not only do you get yourself prepared for an encounter later, but you also can create a level of flow from the events leading up to combat. On the other hand, if you are a little more of a DM that likes making the PCs second-guess their decisions this also works because they automatically think that any action could instigate the start of an encounter whether there actually is an encounter planned or not.
If you find that the flow of your campaign gets broken by the commotion of initiative, then you can try this in your group. I found that this is pretty effective, even in sessions with multiple combats, this way they complete one encounter and then you have them roll again for their next encounter regardless if there is one planned or not. Generally as a house rule, I have players re-roll their initiative if we go into a new session without the initiative roll being used, but not if they are still mid-combat (though we try to not end a session mid-combat if possible).