You should have a line that says <Directory /Library/WebServer/ (etc)/> SOMEWHERE in your httpd.conf - it doesn't have to be exactly the same. The instructions assume you're using the Apple supplied Apache, so if you're using one built from Fink or so forth, the specifics may be a bit different.
If you can't find anything similar, do a search for "Directory" and tell me all the instances that you find.
As for your mod_perl questions, no, they don't really need to be placed anywhere specific, but make sure they're outside any other containers (ie,. you wouldn't want to place them in a <Directory> container).