update, just checked the FSM (thanks, hondahookup!) and this info is on page 378, or 13-28. it simply says to drive the seal into the clutch housing, and then if you look closely at the diagram in step #3 you can see that the seal is indeed bottomed out. the top edge of the housing where the seal is tapped in is beveled, and in the same diagram you can also see that the side of the seal which faces the bearing is at the bottom of the bevel. this is what i found when i installed this seal today so it looks like i have the seal installed to the correct depth.
here's the link to the FSM for anyone who wants it.
Honda Civic Service Manual 1992 - 1995 - Downloads - Hondahookup.com