When you run FreeCap for the first time it will probably look like this: all empty. That's alright, we need to configure it first. So click on File, Settings. All you need to fill in is the proxy protocol and the proxy server as shown on the second picture (click on the picture to enlarge).
When done, you need to create launch icons for all applications that you wish to use through FreeCapand of course Your Freedom. Choose File, New application and a window like the one below will open up. Give the icon a name ("profile name", the name of the game or the application is probably a good choice). Then click on "Browse" and find the executable that you need to run in order to play the game or run the application. If you don't know how to do this but have an icon on the desktop that you would normally use to run the game or the app, right-click on it and choose Properties. Copy the content of the "Target" field into FreeCap's "Program path" field. Also, configure the application's or game's home path -- the installation directory is fine. (You can copy this from the desktop link properties as well.)
When done, click OK and an icon will appear, just like in the last image. To run the application or the game through Your Freedom and FreeCap, start Your Freedom first and connect to the server, then start FreeCap if it is not already running, then double-click on the game or application icon in the FreeCap window instead of using the start menu or the desktop icon.