It's done on the Movement definition screen. After you input the number of tables you will see some extra controls appear on the movement screen. One of these is labelled "Missing Pair". To the right of that is a number, which is defaulted to 0 to indicate there is no missing pair. Up and down arrows to the right allow you to adjust that value to set a table number if you have a missing pair. There are also a pair of controls labelled "N/S" and "E/W" which enable you to set the direction of the missing pair.
Note that in the case of a N/S missing pair you currently have to input the player names for the corresponding E/W pair in BridgeScore. In the next release of BridgePal Server it will be possible to enter or correct player numbers on BridgePal at the start of any round, so the numbers of the E/W pair who started at that table can be input at the start of round 2.