I also use a small bowl, or rather a saucer. I tap the amount I need into the raised portion of the saucer (where the cup would sit) and swirl there. This way I can also mix different things together if I need to. I make my own liquid concealer this way, using a bit of liquid primer and a mineral concealer.
I have also found the using a flocked sponge cuts down on the mess hugely. I use a sponge when I feel that I need more coverage. I have never used BE, but all of the tips that everyone is giving can apply to any brand of MMU.
Janet