I want to join the two cylinders (1 and 2) at an angle as shown below. What is the best way to do this in Blender and still get good topology? Thanks.
Ok, add up a 3 edge loops, wher you want to join the smaller cylinder. Select the center vertex as dipicted in pictures, put 3d cursor on vertex. delete the vertex, add a circle of 8 vertices or as you wish. now join the circles vertices with cylinders. extrude the resulting hole to your liking.
I would rather use a boolean modifier
What dukejib said would be the way that I do it. Booleans in Blender are somewhat horrible and leave undesirable meshes, so a little extra time in the modeling process can pay off big time.