A step is ANY ability you use during a craft. You only waste manipulation if at the end of any of the next 3 steps the item durability is at maximum.

For example, if you use Manipulation at 20/40, then you use steady hand (30/40), great strides (40/40), ingenuity (40/40). The last 10 durability that manipulation would have restored after the last skill is wasted because you did not use any abilities that cost durability.

If instead you use Manipulation at 20/40, then steady hands (30/40), great strides (40/40), advanced touch (40/40), nothing is wasted. The advanced touch cost 10 durability, but that is then immediately restored by manipulation.

Note that if you use Manipulation at 10/40, then use advance touch, you will FAIL the synth, because the advanced touch will have taken your durability to 0/40, and when that happens your synth fails (even though Manipulation would have restored it back to 10/40).