I've always done em' separately too. It just seems easier in the long run, but, I could be wrong. I will say this though: last time I left the entire motor assembled, accesories and all, and pulled it out as one unit. That was no big deal, as long as someone's there to hold AC lines out of the way, etc.
And, I assume you know to either remove the hood completely, or at least unbolt it from the hood shocks, so it can be layed back further. It makes it a whole lot easier to get out, and you won't end up putting reverse dimples in the hood if you peg it with the motor and such.