It seems what you did was you edited the config file, to add another channel, and then you ./eggdrop MyBot.conf to start it again.. If you type "ps x" at the shell prompt, (without the quotes) you will see something similar to the following:
[peakoil@peakoilchat eggdrop]$ ps x
PID TTY STAT TIME COMMAND
16160 ? S 0:33 ./eggdrop opec.conf
29866 pts/3 S 0:00 bash
29881 pts/3 R+ 0:00 ps x
If you see two lines with ./eggdrop in it, that means you have your bot running twice. To end the processes of the bots type "kill -9 PIDNUMBER", replacing PIDNUMBER with the number you see at the left hand side of the screen, beside the ./eggdrop line. In my case, it would be "kill -9 16160". When you kill the process, the bot will drop off line. You will then need to restart your bot, but only do it once this time. (Another way, possibly easier for you, is to connect to the party line and simply type .die)
*Edit: You only need to do this if you have 2 instances of your bot running.. It would look something like this:
[peakoil@peakoilchat eggdrop]$ ps x
PID TTY STAT TIME COMMAND
16160 ? S 0:33 ./eggdrop opec.conf
25560 ? S 0:33 ./eggdrop opec.conf
29866 pts/3 S 0:00 bash
29881 pts/3 R+ 0:00 ps x
Now, to answer your question, you only need one eggdrop, you can make it join multiple channels. I'm not aware of any limit to how many channels a bot can sit on either. You can easily add channels by connecting to the bot's partyline, and typing ".+chan #newchannel" to make it join a new channel, and to leave a channel, type ".-chan #oldchannel"