I assume that once you do either of these:
Add one die to a column or
take all dice back from a column,
you re-roll all the dice not yet played again?
Yes, if you wish you can stop and look how your teammates are doing and on what is the volunteer working on. Remember, that if you cannot place a die, but you rolled, you have to take back all the dice. I found it to be very disturbing if going for the perfect score in one of the collums. Rerolled those dice 3 times.
Also when scoring it seems like you take the number of die pips on the 2nd to highest die in each color for the score?
So if there just two dice in a column (a 5 on bottom and a 6 in the "2" spot) that would be a 6?
No, you look on the value in the collum, the dice are only there to see how good you did, not the value of the dice (except for 6 which gives you + 1). In your example, a 5 and 6 would land you with 2 points + 1 for the 6.