All Clover Configurator does is mount the EFI partition, and give user-friendly way of editing the config.plist (an OS X properties list file) located in clover. Generally clover is used only for OS X, since well, as far as I'm aware it was created specifically with Hackintoshes in mind.
You can mount the clover EFI partition in Windows by doing the following:
Open command prompt as Administrator.
Run the following commands:
diskpart
list disk
(If you have more than one disk, take note of which one you installed the Clover EFI onto.)
select disk #
(where # is the disk number of the disk with Clover)
list partition
select partition x
(x for the clover partition- for me, the clover partition was 200MB. For some, it's 100MB. The title is usually "Unknown", but if you see none of this, you probably chose the wrong drive.)
assign letter=s
(or whatever drive letter you want, as long as it isn't already occupied)
exit
You can close command prompt.
Now, you should see an EFI drive in Windows. You won't be able to access this drive through explorer- instead, you need to do it through Task Manager.
To access the drive in Task Manager, click Run new task, and in the window that pops up, in the bottom right click Browse.
You can now select the EFI drive.
To access the config.plist file, you want to head to EFI/EFI/CLOVER/config.plist - copy this to your desktop, or whatever directory you please, and edit this with whatever rich text editor you use. A large portion of it is going to be related to Mac OS X and Hackintoshes, but you can ignore all of this.
CTRL-F to find something called "GUI", under that, to add things to the Clover boot screen, you're going to want to add entries similar to this:
<key>GUI</key>
<dict>
<key>Custom</key>
<dict>
<key>Entries</key>
<array>
<dict>
<key>Disabled</key>
<false/>
<key>Ignore</key>
<false/>
<key>Path</key>
<string>\EFI\ubuntu\grubx64.efi</string>
<key>Title</key>
<string>Ubuntu</string>
<key>Type</key>
<string>All</string>
<key>VolumeType</key>
<string>Internal</string>
</dict>
<dict>
<key>Disabled</key>
<false/>
<key>Ignore</key>
<false/>
<key>Path</key>
<string>\EFI\Microsoft\Boot\example.efi</string>
<key>Title</key>
<string>Windows</string>
<key>Type</key>
<string>Windows</string>
<key>VolumeType</key>
<string>Internal</string>
</dict>
</array>
</dict>
It's quite tricky to edit plists without something that can make sure that the file is formatted correctly, but each new entry will look something like this:
<dict>
<key>Disabled</key>
<false/>
<key>Ignore</key>
<false/>
<key>Path</key>
<string>\EFI\operatingsystem\example.efi</string>
<key>Title</key>
<string>Whatever you want it to show up as</string>
<key>Type</key>
<string>Windows or All</string>
<key>VolumeType</key>
<string>Internal</string>
</dict>
The process isn't this simple; I've only outlined a few of the steps. For a more detailed guide, click here.
This person knows more about this than I do, and they have a far more similar setup- they're running Kali, Ubuntu, Windows and OS X.
Best of luck to you!