Even if I do that and go full screen the other monitor I have connected will still go dark and I cant use it.
It shouldn't if you're using native Fullscreen mode. If it still is, you're either not actually using the right Fullscreen mode or something is wrong with your system.
Do you see this icon in the titlebar?
And when you go into Mission Control with VLC full screened, does it get its own space at the top? If not, then it's not enabled correctly. For me, the latest version of VLC enabled "Lion Fullscreen" automatically. Do you have the latest version of VLC? 2.1.2 is the latest version.
Edit: I really wish 10.9.2 would come out already. The Finder is so screwed up, I want to know if they fixed the weird refreshing problems. Folders will not update themselves in a timely manner anymore until I force refresh them by renaming a file. For instance the folder might show a list of files that don't exist anymore, but for some reason the Finder is retaining the information. If I rename a file, it will force the folder to refresh its contents. In Windows you can press F5 to refresh a folder, but OS X/Mac OS Classic never needed to do this until now for some reason.
Interestingly it seems to be a filesystem problem, not a Finder problem specifically. Because even the /Volumes folder is retaining contents. Sometimes when I wake from sleep, CCC thinks an external HDD is connected and runs my "Run when disk is reconnected" task even though the drive isn't connected. At first I had no idea why it would think this, but now it occurs to me that it's probably related to the above problem in that the Volumes folder actually thinks the aliases still exist. So when CCC sees the aliases there it runs the tasks. Even though there's no way for it to actually run.
I hope 10.9.2 is a big update that fixes everything. I have a feeling I'm getting my hopes up.
My other biggest problem is how shitty Screen Sharing.app is. I tried using Chicken of the VNC but it is all fucked up. Screen Sharing works fine for me when it works. But it seems to be like an old car in that it takes sometimes 3 launches in order to get it to open an alias. And when it does, the window is so small in the center of the screen. *sigh*