Running OS on one HDD and everything else off of other HDD

The programs still need to be installed from within the OS on the smaller drive, unless you want to manually go in and copy the Start menu directory tree from one drive to the other, and then also manually edit each shortcut's path to make sure it's correct. Often times you also find larger programs, like MS Office, may not function properly if you try and run them from another drive where you installed it under a different OS. You should reinstall each program and just point it at the other drive when asked during the installation process.