The sound card in your laptop will be completely bypassed by the modi USB. The windows system volume will be controlling the modi USB level directly.
Set it to 100% (the windows system volume in the system tray for the modi USB output).
Use replay gain to set your volume to be consistent through out your music collection so you don't have to be fiddling with the volume all the time.
If you haven't already done this, you must do it, it will prevent having to adjust the volume after every song and throwing shoes at it.
Set your software player for music to 100%.
The only place you will control your volume from is your software player(s).
You can leave this at 100% always since you will use replay gain so that all songs will have the same loudness.
Next, set the physical volume on your magni to about your normal listening volume and leave it there always (* see below).
This is what I do and it works for me.
* Instead of setting the magni volume to your normal listening volume, you can set it to say 150% normal listening volume, to give you some leeway for when you listen to youtube etc. that don't have replay gain applied and which may require a higher volume. You then use the volume control in the software player (youtube in the case) to control the volume as required. Your software player for music won't be at 100% anymore in this case too, set to it to match your normal listening volume and leave it there always.
Some other points...
You can set the modi to 24bit, and according to that thread you linked, it will then allow you to reduce the volume (anywhere in software) with no data loss.
There is a lot of ifs and buts in that thread so I am not sure it's 100% accurate but it can't hurt to do that (but it might cause drop outs if your pc is slow).
I don't notice any difference if its 16 or 24 bit.
With regards to the EQ volume, its not really there to be used as a traditional volume.
Your EQ setting (nicholars file) is reducing all the frequencies (everything is below the 0dB y-axis), so you should leave the volume at 0dB always.
If you had frequencies being boosted in the EQ, say the bass was boosted by +4dB, you would then reduce the volume by a matching -4dB to keep the overall frequencies always at or below 0dB. This is to prevent your amplifier from clipping and causing distortion.