While you are waiting for the water to boil, it is OK to cover the pot with a lid. However, once the water has begun to boil and the pasta has been added, the cover should be removed to avoid the water from boiling over.
Prior to starting, boil some water. Always, and I mean always, bring the water to a boil first before dropping the noodles into the pot. It is not recommended to put the noodles in first since the strands will ultimately get mushy and sticky. The addition of noodles to the water immediately lowers the temperature of the water, causing clumps to develop.