I always combine my last 2 shakes of the day into 1 large one which I drink slowly over 20 minutes or so. the first few times this felt like a lot to drink in a short time, and gave me a bit of a funny stomach, but now totally used to it and no side effects at all.
I agree that having 1 in the morning when you wake up is good habit forming, I too can't really stomach anything for the first few hours after I wake up but I force myself to have "breakfast" as I want to be able to have a real breakfast once I'm back on food, as it's good for you and important to get your metabolism and brain going.
that said, while on the packs I really don't think it matter when you have them, so long as you have them all each day you are getting the vits&mins you need, so do what works for you
PS My LLC advised that if you don't have a pack for breakfast, it's best to drink a pint of warm water as this too will get your body going into "day" mode, though I don't know if that's true or not.