Both of the types of speedskating boots that I tried on had two laces per boot. The long lace goes from the toe to the end of the top part of the foot while the short lace goes from the end of the top part of the foot to the top of the ankle. The idea behind using two laces is that the fit of the boot can be adjusted independently top and bottom. Nick said that the most important part to do up tightly is the area across the top surface of the foot. The boot will mold to the heel and hold that part in on its own so that leaves the top of the foot as the part the laces most need to hold in.
It is important when wearing speedskating boots that your heel is locked in to the heel of the boot. Accordingly, put the boot on, and then whack the heel of the boot on something solid to be sure that your foot is all the way in and your heel is exactly snuggled into the heel of the boot.