Weekends are the most crowded times, followed by commuter times on working days.
Prior to the merge point there are several exits for San Ysidro - this is where you should take care of insurance and money exchange, if you haven't already done so. I almost always use the San Ysidro crossing as I find it more convenient to the toll road, my usual route south. Ease of crossing Often very crowded. Much less crowded. Right on the way.