I don't think the name Baal is related to El. It is spelled with an AYIN while El has an ALEF.
There are conflicting theories about what the name El meant in mesopotamian paganism. Some claim that it is the name of a specific god, supposedly superior to the rest of the pantheon, later adopted as the monotheistic god of judaism. Others think that it is a generic name for a deity and when used without qualification it simply means the patron god of the speaker's tribe. According to this theory El did refer to Baal for some.