TotalTerminal doesn't work with full-screen apps
This is a known issue and the author doesn't plan to fix it.


  I encourage someone to go further and implement it because personally I don't use fullscreen apps right now and I don't plan to fix this anytime soon.


Luckily, there is a workaround described by vvlad.


  As an workaround you can set LSUIElement in Terminal's Info.plist


It has several drawbacks but otherwise works like a charm:


  
  Terminal no longer shows on Dock;
  There is a space the size of the top bar on top of every TotalTerminal visor opened on fullscreen apps windows;
  You can no longer ⌘⇥ to regular Terminal windows;
  You cannot Force Kill Terminal process.
  


This is how it will look like:



How It Works


  LSUIElement (String - Mac OS X) specifies whether the application runs as an agent application. If this key is set to “1”, Launch Services runs the application as an agent application. Agent applications do not appear in the Dock or in the Force Quit window. Although they typically run as background applications, they can come to the foreground to present a user interface if desired. A click on a window belonging to an agent application brings that application forward to handle events.
  
  The Dock and loginwindow are two applications that run as agent applications.


How to Do It


Open Terminal (assuming you already have TotalTerminal installed)
Run sudo nano /Applications/Utilities/Terminal.app/Contents/Info.plist
Add these two lines right after opening &lt;dict&gt; tag:

&lt;key&gt;LSUIElement&lt;/key&gt;
&lt;true /&gt;

Save and close the file by pressing ^O Enter ^X
Quit Terminal and launch it again