Use a ladder to climb up on the roof. In different parts of the country, the winds of the worst weather often come primarily from a single direction. Determine which direction these winds will be coming to batter the roof.
Examine the roof from the direction of the worst winds expected. Identify any dips or rises in the surface that have been left from the building of the roof. Any points that will provide a place where water can run uphill and slip under the shingles must be addressed, as well as any shingles that are buckled or have warped.
Seal the shingles around the three open sides in the areas of concern, using a can of silicone sealant in a caulking gun. Make sure that the sealant makes good contact with the buckled shingles so that there is no longer a gap under the shingle and that the water can't seep back up and under the shingle.
Look at the flashing that is used around vents and chimneys to determine if there is bent or poorly sealed sections where wind and rain can run around or through to reach the underlying roof. This can also cause damage that will eventually require the roof to be replaced. Seal this with the silicone to seal it tightly against leakage.