In my opinion, this is the best and most secure way to link bots, and to create a botnet.

Step 1
   - Pick a Hub bot, a bot which all other bots will link to, I suggest it having the most uptime and being the most secure.
Step 2
   - Find out all the ip's and all the ports for your other bots.
Step 3
   - DCC chat OR telnet to your hub bot.
   - Once your in the bot you will have to add each bot to your hub.
   - These are the commands:
       .+bot BOTNICK x.x.x.x:port (eg: .+bot BOB 123.21.123.45:1234)
       .chpass BOTNICK PASSWD (eg: .chpass BOB bobnewpass)
       .botattr BOTNICK +gs (eg: .botattr BOB +gs)
       .chattr BOTNICK +bfov (eg: .chattr BOB +bfov)
   - Repeat that for all the bots you will want to link to your hub.
Step 4
   - DCC Chat or Telnet to all the bots that you will want to link to the hub.
   - Once your in the bot you will have to add the hub to each of them.
   - These are the commands:
       .+bot HUBNICK x.x.x.x:port (eg: .+bot HUB 123.26.423.43:1234)
       .chpass HUBNICK PASSWD (eg: .chpass HUB hubpass)
       .botattr HUBNICK +ghp (eg: .botattr HUB +ghp)
       .chattr HUBNICK +bfov (eg: .chattr HUB +bfov)
Step 5
   - That's it, your bots will now automatically link.

If you have any problems, contact your shell's support team.