Yeah, just base the majority as pairs, then a few militia types in threes, just for the odd scenario where you might need them.
Basically, the overwhelming majority of skirmishers are going to be reasonably well-trained in the role (even if they're from a unit that might not be so good fighting in line), so roll 1d6 per pair of figures. But a few based in threes are always handy to have (poor skirmishers roll 1d6 per three figures).
In my own collection, in terms of skirmishers I've got:
Enough British LI skirmishers to replace one of the two formed LI battalions (12 pairs).
Enough Queen's Rangers skirmishers to deploy the whole battalion as such (10 pairs).
Some skirmishing 16th Light Dragoon LI Troop (3 pairs).
Some skirmishing Highlanders (2 pairs).
Some skirmishing Guards Light Coy (3 pairs).
On the rebel side I've got a load of skirmishing riflemen (10 pairs).
Some skirmishing Continentals (3 pairs).
Some skirmishing Militia (3 triples).
Some skirmishing States Line (3 triples).
I could probably use a few triples to represent the less able Loyalist regiments and a few more pairs of Continental skirmishers.