Since you currently have the wimpy JBL E250 sub, you might consider setting your mains to LARGE and sub to BOTH to supplement the low end. It would be interesting to see if your M60's play lower than your current sub.
Also, most receivers, including your Yamaha have a single crossover frequency that applies to all speakers. HK receivers and high end models from a few other manufacturers have seperate crossovers for the fronts, center, and surrounds. I am not aware of any "factory defaults" that override the crossover setting, except for THX modes which default to 80 Hz.