The color of a side depends on the color of the centrer sticker. Ex: the red side is the side with the red sticker in the middle. For this reason, when prompted to enter in the colors of a side, you will not need to enter in the center sticker. You must, however, pay close attention to the colors of the adjacents sides. Ex: you are entering a yellow corner sticker on the the white side, you notice that this piece is adjacent to the green side and the red side (determined by the colors of their center stickers), it is important the yellow sticker be placed in the same corner on the virtual cube.
To ensure this, notice the virtual cube as it is oriented on screen and orient the actual cube the same way and entering the colors will go quickly and correctly.
When you are satisfied that you have entered in a sides colors correctly, click the middle sticker and you will be taken to the next side, The virtual cube will also re-orient itself to assist with input for that side. When the middle sticker for the last cube is clicked, the cube will automatically solve itself.
If you make an error when entering the sticker colors, the cube may: not do anything, or, the cube may seem to have too many red squares, or, there may be no color at all. If any of these happen, refresh the page and start over.
After the cube solves itself, the moves will be displayed so you can solve your own.