Hi Sleepers Hill,
The answer to questions like this is usually, do whatever is most comfortable to you. There's really no wrong way to play the Em, unless you're playing it with your pinky or something, but even then, maybe there's a good reason for that!
I think that the important thing is, you have the versatility to play ith both ways. However, for the sake of playing the actual song, you said that playing the Em with your middle and ringer finger makes the transition to B7 a lot easier, so I would stick with that for the purposes of the song.
If you can play it, and play it well, play it!
That's all there is to it.
Best,
Billy