That's not how you "condition" a lead-acid battery...That's how you ruin them...No wonder people are only getting 3 years from their batteries. Your charger will automatically run an Equalize charge when necessary or about every month that should help clean the lead-sulfate crystals off the battery plates. The charger ramps up the voltage for about 4-5 hours in an attempt to "boil" the plates clean. You may smell a bit of sulfur in the garage when Equalizing occurs and it is perfectly normal.
Believe me - Your Yamaha smart charger is smarter than your salesman