Not a silly question at all. It does all depend on exactly what you’re looking to achieve. There are multiple ways for people to organize and keep their files, some people like to do it manually (myself being one of those) and some like to try and automate the process as much as possible.
Either way, however, will end up with you making folders over there on that second hard drive.
If you’re looking to just have your Music, Videos, Documents and Pictures over there, then that’s certainly something you can do within Windows. These are often called “Libraries”, these are just fancy terms for Windows to link files together and know exactly what’s stored within them. For example your Music Folder is a library for Music, meaning Windows knows that’s where to store your music, and how to present that folder to you.
You can change and move those locations whenever you please, I’ve only got a Windows 10 Desktop at home, so the following instructions are for that:
Word of warning, You do the following at your own discretion and it's always best to back up your files before changing the location of lots of them!
####First you’ll need to navigate to Cortana (Search box at the bottom) and type in %userprofile%
####Next you’ll need to locate your libaries (in this example “Downloads”) and then right click them, and select properties
####Within here you’ll be presented with a few tabs, you’ll need to select the “Location” tab. From here we can select to Move that location
####Next we navigate to a new file location, here you’ll see I’ve moved to my Spare drive and create a “MovingTest” folder. Once done hit Select Folder
####Finally you’ll get a nice little warning from Windows explaining that they recommend moving all of your files, as well as confirming your decision. Once you hit Yes, that will all be set as your default Library Location for Downloads.
You’ll need to do this with each of your Libraries (Music, Documents and so forth) and making new Folders for them on your second drive, or wherever you want them to be stored.
With Files and Libraries out of the way; if you’re looking to have a place to install Programs to, this really depends upon the program you’re installing and how you’re installing it.
While there is no “default install” location for programs that you can change within Windows, you have to change it each time your setup an application. Generally you’ll either be presented with where you want to install it at the beginning (allowing you to browse to a new location, such as a second hard drive), or you may have to select the Custom, or Advanced installation instructions to see those options.
Unfortunately pictures won’t do you much good here, as each application is developed differently with no, one universal look of an installer (or whether those options even exist for that particular application).
Hopefully that covers the basics for you. There are lots of different ways, and other options for changing file locations and folders, this is just the easiest and more basic way to do so. As I said before, a lot of people like to just do it manually and feel like they have a little more control over the entire process.