The same way that you do colors normally. The only thing you MUST keep in mind is that you are limited to 72-80 characters max by the IRCd. Everything past that point is chopped off and never sent.
DALnet: #HelpDesk and #m[color:#FF0000]IR[color:#EEEE00]C
Edit it in mIRC ... /load -rs it as a remote script file so you can enter the colors you want using Ctrl-K like you normally would. You can even /play -e (to echo it, rather than /say it) it to a window to see how it's going to turn out.
DALnet: #HelpDesk and #m[color:#FF0000]IR[color:#EEEE00]C