Oops, misread you question, I see you already have dual boot going on, well in Windows2000 without the help of 3rd party apps, both installations need to be able to read the system partition (normally the C: drive, boot.ini, NTdetect, and NTldr are all stored there) so if that is also where one of the installs IS, then to truly get what you need you'll have to have both of your installs on different partitions, so you'll have to have the at a minimum three partitions as the 2 boot partitions (where the OS is installed) both need to access the system partition (where the hardware specific files are). but there are no provisions I know of to hide completely one of those installs, they would just be segregated in their own partitions.
A product like PowerQuest's Partition Magic can do that for you, it comes with a applet call Boot Magic which can help with your hide/unhide wishes as you boot to each. So it could Hide the first installation completely and make active another partitionwith it's own boot menu.
http://www.powerquest.com/partitionmagic/
Lee