If you have two units not together, and you want to attack a city, can you have them meet at the city, or do they need to be together before going into a city to fight?
No, you cannot move your next figure until you end a movment of previous. This is somewhere in the rulebook in section about moving.
I was also wondering if army groups can cross over other army groups you have. For example, If I have a stacking limit of two, and I have two flags that already moved, can I go through that square with two other flags together, or is that not allowed because going through that square exceeds my stacking limit for a moment?
It is hard question (good for game designer). If you want cross some square you have to physically touch it (except when you are able to fly), and at the moment your figure remain there. Personally, I belive that stacking limit wasn't created for that situation, however Council of Elders (me and my friends
) decided to rule with first option.