From the description it seems like setting "Extra" to "-2" and telling it to keep the highest x (so if you want 6d6 rerolling ones and twos, then extra = -2, keep = 6) should do it, but I can't seem to get it to work.
Not sure if its not working properly or I'm not doing it properly.
I don't think you're doing it wrong. A negative value for Extra doesn't seem to be working as advertised.
For the "reroll 1's and 2's" thing I think the best bet is do roll d4+2.
For something like "4d6, keep the highest 3, reroll 1's and 2's", which is somewhat common, you'd do:
4d4, keep the highest 3, then add 2 to each. (Or 6 to the total, of course.)
Or on the Elliquiy die roller: