#1 - Install fenders with long mud flaps. The mud flap on the front wheel will keep water from splashing on the bottom bracket and your feet. Of course, that won't help if you ride through a puddle deeper than your bottom bracket.

#2 - Here in the Northwest, it rains so often that I would never leave my bike sitting outside all day, day after day. I've been fortunate enough to be able to lock my bike in a parking garage. Some people find an overhanging roof eave or canopy to lock their bikes.