"I have a green flag,, and she has a green flag too."
Translation:Mi havas verdan flagon, kaj ankaŭ ŝi havas verdan flagon.
I always forget why, but why does ankaux have to come infront again?
It emphasises the thing it comes in front of.
So "Ankaŭ ŝi havas verdan flagon" would mean "not only do I have a green flag, but she does too".
"Ŝi ankaŭ havas verdan flagon" could mean "She not only likes green flags, she has one, too". (Though I would also use it as a general sentence, even for the "not just I do but she does as well" case.)
"Ŝi havas ankaŭ verdan flagon" could mean "She has not only a blue flag but a green one as well", or "She has not only a car but also a green flag".