I generally keep about headroom at about -6dB (no less than -3dB at peak) on input for most material. For electric guitars I usually take in a DI feed post-pedals and a separate mic’d amp as separate tracks then bounce the tracks into a single blend at mix time prior to adding an insert chain and sends instead of mixing them separately.
For acoustic guitars I set up a stereo pair of small condensers one point at the body the other pointed at the 12th fret and will take in a DI if the guitar has a 1/4" output.
For bass I’ll take in DI (post-pedal if applicable) and DI from an amp head. Depending upon what kind of space we’re recording in, I may mic the cabinet. Generally in smaller places I won’t use a cabinet as it doesn’t work out too well with the low frequencies.
Depending on the player I might add just a touch of compression on input to prevent clipping without putting that in the mind of the player. It’s up to the recording engineer to get a good performance from the artist and making sure the signal doesn’t clip but to also not affect the sound of the instrument on input.
I wrote an entire essay here on an experience I had with the band I was working with a couple of years ago if you want to check it out: Recording, Mixing, Mastering live instruments for an album in a home studio