When I filed my back returns, I used the 1116 Foreign Tax Credit when I had multiple sources of income.
Other years when I only had one source of earned income then I used the 2555.
She only files one 1040 and one 2555. Just add the salaries from the two jobs together and report on a single form. If both jobs were outside the US and she qualifies for the FEIE, she can take it against the combined total of her earned income from outside the US.
In the part where it asks what country you live in, include both. Include both employers and their addresses in the part that asks that information.