Draw Semi-transparent texture.

Let x be the first texture.

I want to draw a semi-transparent texture on other texture such that both textures are visible.

Can I use SetPixel/SetPixels

Make your material with a transparent shader (Legacy tab in shader area). Then when you are using SetPixel, make the color like this:

Color c = new Color(red,blue,green,alpha/transparency);
//do your setPixel actions here