So, I should copy it into all of those places? Also, is it likely I'll get errors if I simply try to upgrade ISPConfig and upgrade spamAssassin in the process? I'm running ISPConfig 2.2.9 on SuSe 9.2. Is there a way to make sure everything that's needed is installed? I am always scared to upgrade because I've gotten errors before.
You can try those directories one-by-one. Normally there shouldn't be any problems, but to go sure, you should back up the directories /home/admispconfig and /root/ispconfig as well as the ISPConfig MySQL database.