Many of our planks have knots in them. The dark swirls add interest to the pattern of the grain and can be a delightful feature of the wood. They are however a pain to work as they are tougher than the surrounding wood.
We got our planks planed and thicknessed by the timber yard as the equipment to do so is beyond the means of most amateur wood workers. When we started to try and clamp the table top together we discovered that one plank was not square. It appeared to have hit a knot when having the edges planed and twisted slightly (you can see the gap between the square and the wood in the top photograph). This wasn't the wood moving for the top remained flat. We therefore had to re-straighten the edges. Without the proper machinery the most accurate we could do was use a router to re-cut the 90 degree edge. Several sessions of carefully measuring, clamping a guide, cutting into the edge of the wood millimetre at a time and remeasuring later we had a square plank again.
Next: 4. Starting at the Top