It would help more if you would also show us the script you're currently using.
To hide all channel windows on all networks, you could use
alias hideall {
scon -at1 hide $1
}
alias -l hide {
var %a = 1, %b = $chan(0)
while %a <= %b {
window -h $chan(%a)
inc %a
}
if $1 == status {
.window -h "status window"
}
}
Usage: /hideall
/hideall status
The second usage will also hide your status windows in all versions of mIRC except 6.2 (untested with 6.3)