If you record things with microphones, or plug keys or other electronic instruments into your interface, that is analog and susceptible to to overload without peaking in the digital domain.
If everything you do only involves soft synths and loops, then gain staging will only effect how the plugins you use react. For example, if you use plugins that emulate real hardware devices, running a signal level to them that is higher than the line level equivalent will distort the plugin, just like it would the real piece of hardware.
For actual hybrid systems, you have to use proper gain staging or else the analog equipment will not respond properly.
what is that you do to ensure nothing clips from the very start of the process to the very end? and i know someone will say just turn it down. what i mean is do you allow for that really big hit drummers seem to do only when you hit record or do you set the levels for a take then adjust levels by say 3db lower than the biggest hit so when you have finished recording your biggest peak is -3db or so. or do you aim for a much lower peak level?
For drums and anything else that has a percussive peak and a short decay time, I just set it so that the highest peak is around -6dbfs.
For everything else, I set it so that the sustain of the note is around -18dbfs(about half way up the meter in the DAW). This corresponds to 0dbVU on my analog devices, which is where they were meant to run. That means the signal to noise ratio is the best and the circuitry is at its most linear.
On the analog side, peak level doesn't matter much. On the digital side, sustained level doesn't matter much. Since digital levels are much more forgiving, it's best to optimize the analog levels on the way in.