Dealing with two pairs in early game can be a tough decision, you should always hold the pair for three of a kind or four of a kind.

In general, if you have an unfilled higher pair early game. Hold the higher pair for better chances to fill the upper section. You should go for the three and four of a kinds if you have a 4 or higher pair dice. If the higher pair has already been filled, it is still better to hold the lower pair for a chance for early game Yahtzee or higher upper section values.

Example
1-1-6-6-x: Hold 6’s and roll for more 6’s.

If the 6’s have already been filled, hold the 1’s and roll.