[Timo]

I think cutting sounds more transparent and also works within existing sound levels (rather than pushing levels above the red line). Cutting frequencies also gives you the ability to surgically home in on any unwanted or annoying frequencies (using narrow Q/bandwidth values) and effectively remove them. This stops the Virus from eating all the available frequency headroom so other sounds are better able to sit with it.

Boosting employs the character of the EQ to give it a more dramatic shape, but again if you boost the low end freq's you'll also change the sound levels so you have to take this into account and lower the overall patch volume to limit clipping. Boosting higher freq's on the other hand have less influence on sound levels so you can often use these to give the patch emphasis in a mix (if needed) without necessarily affecting the overall level.

I have an Indigo v1 so no internal EQ here (although I also often use a band-reject filter in a patch for culling honky frequences within the patch itself, sometimes with key-tracking if needed, and I also use the Saturation- and Distortion-Low/HighPass types for use as global patch roll-offs), but I do use external EQ on Virus parts in the DAW to sit better with other channels.