WINE is just an application that loads windows app binaries and decodes them as would a windows machine and then intercepts the calls to the OS and finds a linux replacement for most of them. Linux will handle quite a lot of windows apps and the more standard the app is the more likely it is to run under WINE.
You can install Windows (and then run any windows app) under virtualization. Thats where the native OS like linux creates a sandbox and essentially creates a bootable computer inside of it and then it can boot windows from a virtual CDRom drive into its virtual memory space. All modern CPUs from both intel and AMD have special instructions in them to handle the virtualization so that they can perform as though they are running the OS on the base system instead of being held in a goldfish bowl. Its not particularly easy for the virtual OS to work out that it is inside of a virtualized container so thats why people like to use them for testing out viruses and so on. Also, when you buy web space you often get a whole machine as your web site. Only its not a whole machine of course its just the OS in a virtual container and the ISP is running thousands of those.
What you have mouse is two native OS's side by side on the same hard drive. In principle one could see the other but its not likely that they would look since you have partitioned the hard drive for them.
From your point of view tho, you just take a windows app and put on your linux drive area somewhere and then if you click on it then it may run because linux will note that its a windows app right away and then load WINE and hand it off and let it deal with it just like it would hand off a JPG to Gimp or ImageViewer or something similar. If you go back to my challenge entry a few weeks ago with the gold and roman mosaic floor I put up a couple of linux and windows apps to do the 3D stuff. You can try them both. I think I put them up in linux and windows format so one might run native on linux, the other may run only under wine on linux. And under windows one will run native and the other wont run at all because MS have no WINE like app and no intention of letting any other OS in.
You could have run a virtual machine in WIndows tho and install Linux into it which is what I used to do in the old days to get a convenient local linux box to run linux native apps.