Welcome to AE...
I don't know what you mean by 40s style silent movie. Silent movies almost ended overnight with the release of the Jazz Singer in 1927. The 40's were known for Film Noir looks - high contrast, sharp shadows. Silent films also had different visual looks and they were almost always monochromatic. I guess you have your "look" fairly well nailed down.
Now on to your compositing questions. First, almost all, and by that I mean probably more than 99% of all compositing effects are done through a combination of layers, masking and blend modes. If you want some glowing, mystical lights in a forrest with shadows through the trees you'll have to separate the foreground, middle ground and background into layers and put your light effects between the layers. The simple lights in the cloud effect you referenced could be accomplished with a couple of blurred light blue shape layers and the add blend mode. If you wanted that kind of light effect you'll have to put another layer on top of the light effect, and then use some additional layers to generate the rays around the edges of the trees. The most efficient technique depends entirely on the shot. We either need to see your original footage or at least a still frame or similar image to point you in the right direction.
The same thing goes for the lights in the sky. If you want the lights to interact with the footage, like go behind trees, you'll need multiple layers and some matting.
I suggest that you do some studying on the art of compositing and visual effects. The tools (software) may differ, but the idea is almost always the same. Separate the footage into foreground, middle ground, and background layers through the use of masking, procedural mattes, keying, or rotoscope and then put your effects in between the layers.
I would check out some books on Visual Effects. Masters of FX: Behind the Scenes with Geniuses of Visual and Special Effects, available on Amazon is a great book on technique and planning. There are several books on the subject on Amazon that are pretty good. Understanding the techniques of layering and blending pixel values in 90% of the battle, learning the software is about 2%, the rest is just plain hard work.
Show us a couple screenshots and we'll try and point you in the right direction.
The first video you linked is using a Glow effect and animating it so that it overexposes the image. Read up on the Glow effect for more info.
You can achieve the dots in the 2nd video by animating the Position of a circle, created either using a Mask on a Solid or by creating a Shape layer (or an imported graphic, but that's not necessary).
If your circles need to go behind objects in your video, then you will need to create a Matte for them.
If you want the out-of-focus effect shown in that video, you can simulate that with a Camera Lens Blur effect.
Sorry for this issue. Did you ever find a solution? Please let us know if our experts’ advice helped you or if you still need help.