The main thing with flurry of blows is that the damage is combined for purposes of resistances and weaknesses. I'm not aware of any ruleset that allows the automatic combination of damage across multiple attacks. However, the simple process outlined below allows this.
To do this, roll your first and second attacks as normal (using the relevant multi-attack penalties) and if both hit, remove targeting before you roll the first damage so that it just rolls into the chat window but doesn't apply. Then drag the result of the first damage roll to the modifier stack so that the damage is logged as a modifier for the next roll and re-add targeting. Then roll the second damage - the amount from the first roll will be added to the second roll - and as you now have targeting the damage will be applied to the target.
Note: you can quickly disable targeting by clicking the small targeting cross-hairs on the modifier stack beneath the chat window.
So, the steps are:
- Make attacks as normal - apply MAP (Multi Attack Penalties) as required.
- If both attacks hit, click the targeting cross-hairs on the modifier stack so that it's greyed out.
- Roll your first damage, this won't be applied as targeting is disabled at this point.
- Drag/drop the result of the damage roll to the modifier stack so that the total damage of the first roll is shown as a modifier and click the cross-hairs so that they aren't greyed out anymore.
- Roll the second damage.