Marshal settings will usually take precedence over individual unit settings. There are a couple times this won't happen, though:
1) The Marshal is wounded or otherwise not present in the battle, and the Vice Marshal is also not present or able to take command. (Wounded, imprisoned, not present in the region, successfully evading battle, etc.)
2) The marshal for some reason does not take command. I am not sure this still happens. It used to be the case that sometimes a marshal just wouldn't take command. I don't think it was a bug.
3) Sometimes heroes will ignore marshal settings and use their own individual settings.
So even if you plan on using marshal settings for battles, make sure that you also give line settings to your nobles.