Depends on how you run your multi-day tournaments. Are you essentially starting a new tournament on day 2? If you're just continuing the tournament, then the chip counts will be where you left them.
You can also press the "Set Chip Counts" button on the Players tab to set everyone's at once (Ctrl+S from the Game window).
You can't make the TD move the player who is the BB, but you can make the TD move players with respect to the button. In other words, if to balance the tables one player needs to be moved to table 1, seat 3, the TD will choose an eligible player to be moved who is sitting at the same position on another table, with respect to the button. Therefore, the player will be the same number of seats away from the BB as he was before being moved. This will happen automatically if dealer buttons have been placed.