I also have two win 7 installed on two different partitions. There are two ways to make this work:
1. set up the 2nd system from within the 1st win system. I.e., boot into the 1st win 7, and run win 7 setup there. The setup program should create the boot loader menu you need. There will be only one boot loader, residing on the 1st win system's base hard drive.
2. set up the 2nd system by booting from the win 7 DVD (or thumb drive). There will be two boot loaders, each on each win system's base hard drive. There's no boot loader menu to choose from the two system. Instead, you choose which system to boot into by telling the BIOS which HD to boot from. Most modern BIOS allows you to do so, I believe, by hitting a hotkey (F8 for my ASUS motherboard/AMI BIOS).
Win 7 setup program searches for a current Windows boot loader on the default boot drive when setting up a new system, and adds to it if it finds one. For the 2nd method to work, as a result, you need to set the 2nd HD as the "default boot drive" (1st priority) in BIOS when setting up the 2nd system, otherwise win setup would find the boot loader on the 1st HD and add the 2nd system to it (creating a boot time menu). The result would be the same as the 1st method. That could be what you want, but if that's the case it's easier to do it the 1st way (installing from within the 1st system), for it installs faster that way.
Note that you can create a separate boot loader on the 2nd HD afterward even if you use the 1st method with the "bcdboot" command. So that should be preferred. I took the 2nd route only because of a special condition. My 1st system is on a HD, while the 2nd is on an SSD. Win 7 has some special optimizations for SSD, but I found it didn't apply those optimizations when I install it from within the 1st system.