Virtual and native OS systems - Sierra, Mavericks and Windows/Bootcamp?
In my opinion a set-up covering all three scenarios is possible but it requires a lot of work and the whole thing is probably fragile and won't survive upgrades or special updates of either of the partitions.




Parallels Desktop as well as VMware Fusion allow to use the Boot Camp partition as virtual machine without losing the ability to boot to the physical volume. In the past this feature had some hick-ups though (e.g. loosing Windows activation).
Triple boot macOS 10.12/OS X 10.9/Windows should be covered by one of David Anderson's answers. One answer showing the basic approach can be found here: Installing Ubuntu on Mac with macOS and Windows already installed. Install a basic OS X system (Sierra), install Windows with the Boot Camp Assistant. Resize the Sierra partition without touching the Windows partitions, add a partition for Mavericks and install Mavericks (or backup &amp; resize-clone your current Mavericks partition).
At least in VMware Fusion it's possible to boot another OS X partition as VM with a raw disk device - this is the method also used with the virtualized Boot Camp partition but not documented to work with OS X partitions:


Create a basic OS X 10.9 virtual machine without installing anything. Shutdown the VM and quit VMware Fusion. This will create a vmwarevm bundle. Open the package (right click > Show package bundle).





Open Terminal and enter diskutil list. Determine the partition numbers of the EFI, the Mavericks partition and the Mavericks recovery partition (probably disk0s1, disk0s4 and disk0s5). Unmount the Mavericks volume.
Change directory: cd "/Applications/VMware Fusion.app/Contents/Library/"
Create a raw disk with the disk number and the partition numbers found in the previous step (the EFI partition is required, the recovery partition probably not):

./vmware-rawdiskCreator create /dev/disk0 1,4,5 ~/Desktop/Virtual\ Disk sata


or without recovery partition

./vmware-rawdiskCreator create /dev/disk0 1,4 ~/Desktop/Virtual\ Disk sata


The command will create two files on your desktop: Virtual Disk-pt.vmdk and Virtual Disk.vmdk
Move the files into the 10.9 vmwarevm bundle (and replace the existing Virtual Disk.vmdk file):





Launch VMware Fusion and configure the OS X 10.9 VM (processors/RAM/network - bridged devices). Launch the VM.




This is tested with a full Mavericks system on an external thumb drive using an El Capitan host and it works. Mavericks and El Capitan both were and still are bootable as real systems.

If your SSD contains one or more CoreStorage Volume Groups it's more complicated. I would revert to the standard OS X partition scheme first.




Recommendation:

Virtualize everything except Sierra because a simple error/user mistake in the set-up outlined above may render all systems unbootable.