How do I connect to freenode.net #perl and identify with NickServ

   # in Global tab
   /networks add -type irc Freenode
   # in Freenode tab
   /set nick YourNickHere
   /servers add irc.freenode.net -ident yournamehere -pass secretpasswordhere
   /connect
   # Don't forget to
   /config save

How do I get notifications whenever someone uses the word perl in a channel that isn't on magnet or freenode#perl

   /rules add input not(channel("#perl")) matches("perl"): highlight

Rules are network-specific so just don't do that on Magnet.

How do I set up a command to ban the hostmask for a given nick in the current channel for 24h

You'll have to read the hostmask of the user specifically, but then

   /mode +b ident@host.name.here
   /delay 86400 mode -b ident@host.name.here

Note the lack of "/" on the inner "mode" to "delay"