Practice and patience. And you will join the Brotherhood of Sprue Stretchers.
I use an alcohol burner inherited from my sister. It tends to have an explosive flare-up before settling in to a steady flame. Steely nerves and intense concentration are required to prevent flinching and setting my eyebrows on fire! I took it to a local IPMS meeting to do a sprue stretching demo, and after mentioning the little quirk, the burner suddenly burped out a ball of fire as if on cue. The guys huddled around the table all backed away like when Dan Akroyd switched on his backpack for the first time in "Ghostbusters".
But seriously (but the above story IS true!) learning to control heating the sprue will allow you to consistently stretch different diameters. If you start with sprue carved in different cross sections, the post-stretched sprue will have a similar cross section. I made some knobs by cutting deep grooves around the circumference of a sprue, heated and stretched it, then took thin slices to make the knobs! And stretching hollow tubing will yield fine hollow tubing. To cut these without crushing, insert a small drill with the same diameter as the inside, and roll on a hard surface while pressing down with a sharp hobby knife.