Hi Guys,
Since I have built about 50+ presets most of which are clean, my approach is this. Have your input turned up to about 70 or 80% for single coil pups. For higher gain pups, turn it down and follow the procedure below and then "drive" it to your liking.
On each preset that you use, level each block except for the main amp so that whether bypassed or not, there is no perceivable change in volume. You may have to turn the main amp level down so that you avoid clipping just while you do this. (Thanks to Yek for this suggestion.) The reason for this is that you can create blocks that can be transferrable between presets or made global and your preset will not have the volume affected. The exception is compression which relies on signal levels to determine how much of the effect will influence the volume.
Once you have the other blocks levelled, time to check your output mixer (far right) and ensure your output slide from each channel and your main output are 0 dB unless you need to boost/pad for other reasons. I add about 8dB to certain output channels and leave the main at zeros as I want plenty of headroom on my clean signal and I leave the main to adjust for the venue or on the fly via my mfc.
Finally, if you are using FRFR, set the main output knob on the front panel to 12 o'clock then adjust the amp block level to normal playing level. You should not have any clipping unless your input is too low and you have your amp too high for your target level of sound. Turn the amp down and adjust the input via the OI menu -> audio so that it's driven correctly.
Others can add/subject from my approach but it works for me.