Very important. Pressing bearings in a manner that's not absolutely square can crack or ovalize the BB shell and/or damage the bearing. Riding with unsquare bearings will cause binding, clunking, creaking, and, eventually, damaged bearings and possibly more damage to the frame.

To do the job right you need adapters to hold the bearings square as they're pressed in. Wheels Manufacturing sells sets for specific bearings that work with their presses. Here's the link: Wheels Manufacturing Sealed Bearing Open Bore Adapters. You can talk with a rep to see if their adapters will work with your press.

My advice is to gingerly punch out the improperly set bearings, reset them using the tool properly, and pray that nothing was damaged. You'll know for sure after the bearings go in and you've ridden a few hundred miles.