First thing
Install Windows with only the SSD installed. This is to avoid Windows placing a boot loader on the hard drive.
As for programs, most programs allow you to chose an install location. I think you will be placing most stuff on the ssd
As for keeping 64 bit and 32 bit separated, you do not have to when you custom install them on the other drive. You can if you wish, but I have not seen a need to. Windows keeps them separate to avoid issues(and since some programs have a 32 bit and 64 bit version).
Steam allows you to make a game library on the hard drive to allow you to install games that are too big or do not get a boost from the ssd on the hard drive without any fancy tricks. You will see this option every time you install a game on steam now.
If you have a program that is stubborn you can use this method. do NOT use this method to try to move parts of Windows as it can cause issues.
http://www.tomshardware.com/forum/294557-32-guide-move-software-games-drive-reinstalling
As for all your user folders, you can just goto c : \ your name \ and right click folders like desktop ect and choose a new location.'
So you may have a setup like this
c : windows and games
d : with some folders like Games, Programs, and Your name(or login. just do not do like me. my documents folder is actually a hard drive. this has worked for me, but If i was to start over, I would have used a folder with subfolders for desktop/documents/ect)
An alternative way to move ALL user folders and appdata over to the hard drive would be
this. I have not used this method but other forum users have. Since I have had multi drive setups since before this method was common I just never moved over to this idea as it will not work for me personally(Some of my systems now have the users folders in a network location[makes backup much more easy since all my personal files are in one central location] and not local. I plan to have this for all my future systems).
If you have any other questions, just ask.