Ok, so turn time machine on when you want it to run and turn it off when you don't want it to run. That's what I do.
It solves all of those problems and I know I have multiple backups going back in time rather than relying on my own brain which, if I did that, means I will absolutely forget to back something up eventually because I can't remember every single thing that's on my computer.
The idea of doing it manually is just...
No, I just don't use Time Machine at all. I mean, I only have one Mac, and much of my stuff is either on network drives or external. The stuff on my local HDD is really only place holding. If it gets lost it's no biggie.
Much of the back up is done through Windows anyway (VMWare).
