If you don't have enough ramen or stake ( it's really rare to see someone to be in that state tho) ,fighting those npcsto get your currently-in-lineup ninjas exp but your main character.

Hello.
Please refrain from posting threads like this in News section.
As for your question, exp only contributes to your other ninjas, not your line-up.
so for example, if your main is currently lvl 76, and your 3 other ninjas are lvl 75 (with 99.9% exp), if you battle those ninjas in the map, your 3 other ninjas will earn the exp, but not your main.