Until the 1808 reforms, all line and light battalions received eagles and flags. In 1808, eagles and flags were withdrawn for all except the first battalion, although this seems to have been ignored wherever possible.
Fanions for all battalions in a variety of designs existed from 1809-12, when they were regulated as follows:
1st battalion: Eagle and flag
2nd battalion: White
3rd battalion: Red
4th battalion: Blue
5th battalion: Green
6th battalion: Yellow
However, this change probably only actually happened in the regiments in 1813 as it is known that some regiments carried the earlier, non-standrad, fanions in Russia.
The fanions were supposed to be plain but, this being the French army, colonels managed to acquire decorated ones, often containing an N, a grenade or a hunting horn.
Dutch units carried their own flags (one per battalion) until they were absorbed into the French army, after which they followed French regulations.
Nassauers followed their own regulations and had one flag per battalion.