When you install programs you have the option of telling Windows where to install them. Usually it defaults to C:\program files\... but you can override this and put them on D:.
Most programs allow you to specify where the data is. With programs like Excel when you save your file you have the option of specifying which drive and which folder the data gets stored in. Quickbooks is a bit more complicated but you still have the option of telling it where to put its data.
Also you can tell Windows to move the "My Documents" or whatever your version of Windows calls it to any drive that you want, so you could put that on another drive as well. This is a bit more involved so you should google how to do it for your version of Windows.