The most recent installation documentation is at http://webwork.maa.org/wiki/Installation_Manual_for_2.4_on_Ubuntu_10.04. I think it is up to date. We will update the other installation documentation when things are really finalized which I hope is the current situation.
You are correct that the database initialization has been in flux. It now occurs automatically when you first access the admin course (which you have to do before you can do anything else). If you view problems in images mode (the default) and do not get an error about a missing depths table, then everything should be OK. I assume this is the case for you otherwise you would be reporting errors.
Sorry for the inconvenience.