When you save something, it usually asks you where you want to save it. In those cases, you can choose the SSD. If you want, you can set up a similar folder structure on your HDD and put shortcuts to the corresponding folders in those places on your SSD, which will make all future saving easier.
Some programs have defaults that you can change during or after installation. You can elect to install programs on the HDD, although sometimes you may have to select "Custom" install.
If none of this helps, can you give some more information about your system? Which OS is installed, and on which drive? What are the two drives currently lettered? Do you have a problem navigating to in between them? Other info about your setup?
A really simple answer would be to format both, configure with just the HDD, and then add the SSD, but I'm guessing you don't want to do that.