Yes, micromanagement in Colonization gets ridiculous. I usually either abandon my games half-way through or start cheating to help me out. I don't go crazy with cheating, but I just try to eliminate the micromanagement. I can't be bothered to move tools around for construction and to educate people, so what I do is let my factories produce tools/horses/muskets that spoil because I don't ship them out and instead of it I cheat for as many loads of tools as I produce every turn in any colony.
Same with education. I keep trainers in the amounts I think I need, but don't actually put any students there. I just cheat to make a colonist into a pro whenever I need to. Those two things make life a lot easier when I have a lot of colonies.