@AllHow you handle heavy micro maps? Write down plans manually? Remember everything by heart? Make kind of spreadsheet? Use notes/reminders?
Closest to what I do is use memory but it's a combination of many things. Anticipation plays as much a role.
I doubt there are two players who handle the interface in the exact same way.
No way I open a spreadsheet for solo play
Reminders... never got the hang of those. Ain't the feature really laggy?
Don't wait for pop-ups. Take an area of the map and give orders (might be orders for next turn to a worker – if you've already thought about it, no need to come back to it later). Alternatively, take a theme (insert factory in city queues / move army, etc.) and cover those orders first.
Make queues in cities when it doesn't hurt.
Use F1 to ease specialist management. Use keyboard as much as possible (mouse is too slow). Don't open unnecessary screens. Well, don't click unnecessarily. If you need information, just get it and ease the decision process.
Bright ideas (lol) / Mid-term plans / imperatives can be written on the map via Alt+S ("More workers!" "1 pop whips!", "Forbidden Palace!", "time X + Y!" "change civics", etc.)
Important thing, here, is to avoid any overload (otherwise the map just becomes impossible to read). So those signs are to be erased asap.
Also, a sign might act as a blinker, might make you miss an opportunity because the situation changed and objectives should have been actualized.
What I will do but that is more for the early game is minimize Civ and open an electronic calculator.
Eases a lot the production of the first workers/settlers/wonders.