Quick explanation about modes and their functions. (please read)
Firstly, a mode which is actived is noted + and at the opposed, a mode which is deactived is noted -
I show here 2 sorts of command, because the first one doesn't work sometimes because the channel has been configurated by default on certain mode with Chanserv. You can use the second command only if you've got an access on the channel and if you're logged. The second command'll memorize the change, so you have to restore the channel after the attack by typing - instead +, this principle works for all.

Example:
/msg chanserv set #your_channel mlock +t
/msg chanserv set #your_channel mlock -t

Important modes
t = topic, when that mode is actived, only the opped can't change the topic.
i = invite, with that mode you'll stop an invasion because only peoples who are invited can join the channel. ( /invite guest's_nick #your_channel ).
m = moderate, only peoples voiced and opped 'll be able to speak on the channel.
l = limite, this mode imposes a limite of person on the channel.
s = secret, that mode hides your channel from the /whois.
(If you want to know more about others modes, go on IrcHowToFr)

How to react if bots :

• invade the channel

For these case, i advice to use 3 settles, firstly put the topic on +t, then put the channel on +m and +i modes.

/mode #your_channel +tmi

/msg chanserv set #your_channel mlock +tmi

Then you can voice the peoples that you know and kick/ban the bots.

/!\ Don't forget to restore the channel then, otherwise peoples can't join the channel and won't be able to speak if they're not oped or voiced.

If you think the bots may come back, you can fix a maximal limit of person autorized on the channel, example:

/mode #your_channel +l 51

/msg chanserv set #your_channel mlock +l 51

• flood on the channel

To make stop the bots who speak, you can put the mode +m, this is mean only the peoples voiced or oped 'll be able to speak

/mode #your_channel +m

/msg chanserv set #your_channel mlock +m

/!\ This mode must be used only when it's necessary, don't forget to restore the channel after.

• flood with the topic

You just have to put the topic to +t

/mode #your_channel +t

/msg chanserv set #your_channel mlock +t

• flood you with private message

If bot spams you with some messages, you can tape this command:

/ignore its_nickname

If a lot of bots are spamming you, you can tape this command

/ignore *!*@*

/!\ If you use the second example, don't forget to UNignore because this mean you'll ignore everybody.

• join, quit directly the channel and then you receive a message to visit a site (with virus)

If that thing arrives often, you can put your channel on secret. Most part of bots see your channel in the /whois of the peoples who are above.

/mode #your_channel +s

/msg chanserv set #your_channel mlock +s