It's easy to get carried away and become obsessed with getting the "perfect" tone. Adding a PEQ, IMO, is getting into the realm of trying to attain a 'Mastered' (Recorded) tone. This, again IMO, takes away a lot of the rawness and starts becoming a less believable amp and cab tone- becomes too polished. Sometimes less is more and results in a more 'authentic' tone.
I've settled on using the Cut parameters in the Cab block preamp page (Low Cut @100 Hz, High Cut @10kHz) I found cutting more anywhere else tends to cause presets to sound more sterile, no 'breathiness' or character to them. If the highs still need to be tweaked, in either direction, I'll turn to the Amp block High Treble, Treble and Bright Switch/Cap values. My goal is to remove any harshness but still allow the resonance, harmonics or transients outside of the normal guitar range to come through.
A practical application, even though I have the low cut @100 Hz, I use the Proximity (Cab block) with the Frequency set @60 Hz with the Level @4.00. There is a noticeable difference in the bottom end with vs without the Proximity. Doesn't make much sense to me having the low cut higher, but it's something I've discovered by experimenting with the different parameters.