You will find that supports are trouble no matter what program you use. MeshMixer has a pretty good system and custom placement is fairly easy.
For my needs (unique as they are), I find that creating the supports in the CAD program as a part of the file itself is the best. After a while, you start to understand where the supports are needed and then it's just easier to place them yourself - avoiding the critical features that always seem to get in the way on the auto-gen support programs.
I will usually fully cure the part before removing the supports.