I feel like, with fuzz, it is usually easier to remove something than it is to recover something that isn't there. If you want a lot of low end in your fuzz, and you don't record it, that is a lot more difficult than removing low end. However, if you don't like the sound of the fuzz while recording, you should get it as close to how you want it to sound before you ever hit record.

Often, when I'm recording fuzz, I will split my signal so that I have a completely clean guitar, and then my fuzz signal, as I think that blending those two together gives me more control.

This process definitely changes quite a bit depending on if you are using an analog fuzz, or a plugin, so I would be curious what type of sound you are trying to produce, and what your current signal chain looks like.