As far as I am aware Alpha Manipulation effects are always used in combination with a composite transition. This because Alpha Manipulation is to do with manipulating the so called "alpha-channel" of images and videos. The Alpha channel is data that describes how two images are to be combined (or composited) into one. So you need a composite transition on the timeline to tell Kdenlive that you are compositing the videos from two different tracks into one image.
| This image shows two video tracks with no transition.|
The project monitor shows how the upper track takes precedence when no transition is in play.
| This image shows two video tracks with a composite transition in place but with no Alpha information to tell Kdenlive how to combine the images.|
With composite transition but no alpha info to describe how to composite the picture the top track still takes precedence.
| This image shows the situation with Alpha info now added via the blue screen method.|
The blue screen effect is also known as "Color to alpha"  and all the blue screen effect does is say that where the video is blue the alpha value is 0 (i.e. transparent).
So now that we have alpha information the second tracks image now shows through where the alpha channel says the image should be transparent.
You can also combine two video tracks together using the screen transition (if one of them is filmed on a black background).
The preview in Project monitor might go all strange when you select the composite transition in the time line or the video 1 in the time line. (Reported at bug 2990 and fixed in ver >=0.9.5 of Kdenlive)
What the project monitor looks like when you have just selected the composite transition in the time line. This is not what the rendered video will look like.
To get a look at what the video will render as you need to click Video 1 and then Video 2 in the timeline.