One side of the filter block is the shape of the item pipe connection with four squares, and one is the shape of the general item output. I want to know about the square part and the output part Which part is filtered out, and where does the one that is not filtered out go? Or should I use a filter cover instead of a filter block?
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The Filter Block is like an Extender, but with built in Filtering.
The Side with the Square Dots is the Target where you want the Stuff to end up at. This is where you put the Machine that accepts your filtered Stuff, and then everything works like you would normally expect.
The Sides without anything on them are where you hook up the Input Pipe that contains all the various things that may or may not be able to pass through the Filter.
This is all you need to know, the Side with the 4 Arrows is a special one, you can mostly ignore it. But I will explain below what it does.
So what if your Machine happens to output its Stuff into the Filter itself after it is done processing. Surely it would be a dumb Idea to re-insert it into the Machine, and it would also be quite stupid if the Item or Fluid gets stuck inside the Output Slot of the Machine. This is where the Extenders output Facing comes to play. Anything that is inserted into the Extender/Filter from the Dotted Side will exit to the Output Side, WITHOUT FILTERS APPLIED. You can probably imagine what kind of Setups that might be useful for. 
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