The ones where you click a and then you battle them. Would it be shiny when you are waiting to click a or is it not shiny at that time and then when you are battling it is shiny?
What I mean is that when you are outside of battle, will the Pokemon you click to battle look shiny or just regular colored?
No. The game hasn't set whether it's Shiny or not until you have fought the Pokemon, so it's overworld sprite will remain as normal.