You should not have water on the top. If you caulk and plug them then the water will stay inside the area and rot the wood or delaminate the fiberglass. There should be no water at the top it is the sign of a defective seal.
The window and frame NEED to be removed and resealed to stop water incursion. There is no other cure
You can try removing the top weep holes and using caulk to plug the gap then replace the plugs but that will be a temporary fix and if you do not keep a close eye you could have SERIOUS water damage before you realize you have the problem again