Iron, aluminum dust, tungsten dust, titanium dust, chrome dust, pyrite ore, etc. go in the top of the IBF; coal dust, cells, and the like go in the bottom. So put the clay golem (I assume you're using those) supplying iron on the top face of the block, and the one for coal dust on the bottom. Alternatively, if you're using stone golems, put the marker block corresponding to the golem supplying iron on the top and the marker for the golem with coal dust on the bottom. Extract steel (or whatever ingots, silicon plates, etc.) from the side. I would probably just slap a stone golem on the side of the machine.
For the grinder, I would assume that ores go in the top; water, mercury, etc. go in the bottom, and outputs are drawn from the sides.
The implosion compressor, however, is more complicated. Iridium alloy ingots and gem dusts go in the top, ITNT goes in either of the faces with the ITNT texture, and iridium plates or gems can be pulled out from either of the faces with the explosion texture.