You'd want the flag column(s) to key the index, not column1. Start with whichever flag is more selective. So, either: (flag1, flag2) or (flag2, flag1).

But, as Grant noted, it's hard to imagine the selectivity on flag columns being high enough to get SQL to use a nonclus index.

In theory you could create two separate nonclus indexes, on (flag1, column1) and (flag2, column2) and SQL could seek each separately and join on the results, but it's extremely rare for that to actually happen in reality.