The search mechanism automatically attempts all possible rotations and colors, so don't worry about in which corner you draw. There are four possibilities for each intersection: unset, empty, black, and white. Initially, the board starts out completely unset; this is represented by gray lines. In other words, this intersection will not be used as part of the search. Black stones and white stones are obvious, although they are relative: it will match on reversed colors. Empty intersections are black lines. To switch the mode, click repeatedly in an intersection. The current mode of drawing is shown on the left. Once in a mode, it will stay that way as you click on new intersections until you click somewhere that's already set to your current mode. This sounds complicated, but will quickly make sense as you start to play. (Yes, this system is hokey. The applet won't respond to key events for some reason...)
If the position for which you are searching is on a side, not anchored in the corner, check the "On side" checkbox in the applet. This is left off by default to conserve resources and save time (it takes more energy to search sides than just corners). The program automatically tries to figure out which side you mean by the placement of your search stones. This should work pretty intuitively as long as you keep away from corners on side searches.
Note: please be patient after you click Do Search and only click once. Searches take a lot of time and resources.