Honestly, both.
I use cubedesk as my timer for doing regular solves. It's also nice because you can 1v1 people from around the world.
I use cstimer for drilling certain things, because it has many different scramble presets which is really nice.
If you're looking to use one timer only, i'd go with cstimer because of all of the helpful scramble presets and things like that.
Edit: cubedesk also has an alg trainer, just FYI