The funnels will always pull items out of machines as long as the funnel is placed right next to the machine and there is space on the ground or in the structure the funnel is pointing at. To funnel into a structure, the funnel needs to be right next to that structure so that there isn't a gap between them. (If you are dealing with miners, they need to be placed on top of the vein in such a way that they are sticking out over the vein on the side where you place the funnel, otherwise there will be a gap between the funnel and the miner).
You can hold space while placing to center the miner on the vein (this will ensure that the miner is accessible from all sides), and to automatically place funnels right next to structures.
I hope this helps!