With a little practice a branch can be isolated by briefly stopping the throw ball just after it goes over the targeted branch. Throw with one hand while the line runs through the other, glove is recommended. When the ball passes the branch, the gloved hand squeezes the line briefly, the ball will reverse direction when the line hits the branch, and come back at you.
Practice on this one, if you're not careful, you can get a full wrap or two on the initial reversal and then your throwball may be stuck! As with anything, practice, practice... You also may find that you have a preferred throwline/bag weight combo. All other things being equal, there are some trees that I would use a different method than SRT.