Intentional balk to extend the game

Inning: Top 5th
Outs: 2
Count: 2 Balls 2 Strikes
Runners: R1, R3
Score: Home Team 11 – Visiting Team – 1

The Manager for home team requests time to talk with the pitcher, time was granted. After a brief conference I put the ball back into play. The pitcher immediately committed an egregious balk, nothing close to a pitching motion, nothing close to any motion he used at any point in the game. I suspected that the Manager had told the pitcher to balk so I just look at the pitcher and Manager. The pitcher again committed the same egregious balk. I felt I had no choice but to call the balk and award bases. Note: Previously in the game the visiting teams pitchers were pretty much committing multiple balks on virtually every pitch. It was obvious to the managers that I was being slective on the balks I was calling. In the bottom of the 6th a home team coach told me that the manager did to allow his bench players to bat. As best I can remeber only the DH pair and maybe one other player didn't bat. What should we do, ignore what the manager did or what?