Hello, you're totally right, you should set different fixtures to different channels. For example, imagine you have in EMU just 1 fixture added starting with channel 1. Then if you set up all your the three fixtures to channel 1 - then you will drive them thru the added 1 fixture in EMU.
But if you set up you fixtures in different channels, let's say 1, 23, 48 then you should put your fixtures in EMU in these three channels. See 2 pictures (pic 1: 1 fixture in EMU drives 3 fixtures; pic 2: 3 fixtures in EMU drive 3 fixtures).
In the patch grid it is tired by the first pictogram, see pic 3.