You can do that with table counters as well. In Europe a common 14.1 scoring system is to use 3 counters: Player A score, Player B score and Balls Remaining on Table.
You start with 0 on player A, 0 on player B and 15 on Balls Remaining meaning that there are 15 balls on the table. When player A runs 6 balls, you add 6 balls to player A score, and put 9 on BR counter (there are 9 balls remaining on the table). You add scores to players counters only when inning ends. When racking you add 14 to BR counter (you add 14 balls on the table).
This way you always know how many balls you've run despite how long your run is. If you want to check how many balls you've run any time it's BR score minus the balls left on the table (BR says 68 and there are 12 balls on the table - your run is 68-12=56 at the moment).
This system is very good when you don't have to count the balls the player has made. When you start with Balls Remaining figure, you don't have to count balls one by one.
I had a lengthy discussion on the pros and cons of using beads, and counters with different systems a few years ago here. Not going into there again