I have a copy of the Honda Factory Service Manual for 1996-2000 Civics. Its comments on jacking the vehicle are as follows:
To raise the front, place the floor jack under the radiator support - this location is marked with an arrow and is slightly off-center on our 2000 model. Raise the front, and place jackstands under the jacking flanges on each side, just aft of the front wheels. Lower the car onto the stands.
The procedure is basically the same in the rear. The jack is to be placed under the hook welded to the spare tire well, and the jackstands go under the flanges just forward of the rear wheels. (That hook doesn't look sturdy enough, but the manual is quite specific, and I've done it successfully.)
No mention is made of fitting the flanges into slots so that the weight is supported by the frame members above it.
If one is using a vehicle hoist, the four lifting points are to be the four jacking flanges.