back up all your information. install your smaller drive. delete the partitions on old drive. create a partition on the old drive again. (this will make all the info unreadable) and then load the OS onto the new drive. Windows will creat some files on the slave drive and you will have the OS on the small one.
I have the same setup. I have a 36GB raptor as the OS and a 74GB Raptor as the slave. 99% of all programs out today will let you install them where every you want. you will just have to be careful when you load new programs, and where you want them. they will also create program files on the C drive, so if you have games on the slave and have to reload, you will have to remap it so play it again.
but to do it properly you will basically have to reformat both drive. leaving the old OS on the slave can sometimes cause problems while installing the new one, hence the back-up first