I do my best to figure out which spelling the person used most. But I do often put the alternate spellings in the "Other Last Names" field so that if people search a different spelling, they'll be more likely to find it.
I hear ya, though. On my husband's side, there is Tyrrell, Tirrell, Tirrill, Terrill, Tyrel, Therrill, and more! The spelling can change generation to generation and census to census. One man changed his name from Tirrell to Tyrrell to differentiate himself from all the Tirrells in his area.