I'm sure it's fine to do it manually, if it's something that you check daily. The only problem I think, may be with a larger tank, is when you top off, if you don't put in what evaportated, meaning the same amount of water, then I'm not sure what effect it would have on your salinity, etc.
Because I have the BC, I don't believe there's any way to hook up an ATO to that, so I've never even looked into it. The side of BC has a water line marker, marked min and max. I used a silver Sharpie and marked where my water level should be. When it gets below that line, I fill it until it hits that line. But again, with my closed system, I don't see much evaporation at all, especially not on a daily basis.