it's a mixed bag from my expereince. some apps use a fat installer and absolutely must be rebooted to install both versions x and classic. some other apps will install perfectly from classic within os x. and you only have to reboot classic rather than the whole mac-chine. still others simply won't allow you to install in anything but an os 9 boot.
it's more a matter of what the specific installer will let you do.
the safest bet is always to reboot to 9, but it's not always necessary.