Alignment questions

[micheus]

2. FLATTENING THE END OF A CYLINDER: Question #2: What is the proper way to do this?

I could understand and create a similar shape as you shown, but I think that you are looking for something like the steps bellow.
You probably will no want to use flatten in a situation like this since the command will "put " all the vertices in a plane "placed" in the average of them. So, you probably will need to move the vertices after that in order to put them in the right place.