A third base coach must take each situation into account. When the ball is hit, you'll make your decision to send all runners until a fielder changes that plan. The fielder has to field cleanly, then come up throwing on balance and then make a good throw. Wave like crazy and watch were the throw is going befoe stopping certain runners. The runner behind should be following the lead runner, as should be practiced and preached. After a quick wave to the lead runner, you can still put up a stop for the trailing runner if the throw or situation changes. You can't plan much of what you'll do, just react to the situation. However, you can plan scenarios during practice so that you're players are prepared when the situation arises.
Changing signs depends on the age level. Some teams at the youth level will steal signs and still not be able to do much. Coaches can use that to adjust their defense, but may not be able to change the outcome. At older levels, you can also prepare for sign changes in different innings. You can use certain indicators in even and odd innings. You can use certain ones early in the game then change inning by inning. Just don't over complicate anything. At many levels, sign stealing is overrated anyway.