Not true, all programs (or 99% of them) will ask you where to install. Of course, don't click on "typical" or "recommended" setup. Always select "Custom" setup and the software will ask you for the path where you want to install it, then you can select D:\ instead of C:\ for example.
But I recommend installing the most important programs on the SSD because they will run faster. Of course if the program is too heavy and take up too much space you have no choice to install it somewhere else.
It's also a good idea to disable and delete the hibernation files because they take too much space on C:\ (there are many procedures about that on the Internet just make a search).
Another interesting things to do is to move the location of some system files to the HDD, like "Desktop", "My Documents", "My Pictures", "My Music", etc... in order to maximize the space on your SSD.
If you need to move already installed folders, you can move the folders and create symbolic links. The command in Windows is "mklink /j", but read up on it for a few minutes before you start moving things around.
A lot of programs will want to install on your C: drive by default, so you just have to be diligent about installing them to the other drive if you don't want them on your SSD. Or you can move them afterwards and setup symbolic links.