Most apps/programs will let you choose the install directory/drive. Some files go into the registry for any program, no way to stop that, that I know of.
Modern Apps do not give you a choice on where to install.
I run a 256 GB SSD with Windows 8.1, plus three internal HDDs and I just installed most things in the default place (C drive, SSD). I still have plenty of room. I store things on a HDD, as well as I install all games, on an HDD.
Turn off indexing on the SSD. Some say to set your TEMP folders to another drive.
Yrag told me to use Acronis backup, make a backup everyday, and turn off system restore.
Now, I have a rig, with a UEFI bios, but the OS was not installed in UEFI mode, so secure boot and fast boot aren't involved.
In order to take full advantage of the UEFI bios, you must install the OS in UEFI mode. I do not know how to do that.
I have seen tutorials on how to make a Windows 8.1 disc in UEFI mode but I didn't try doing it.