I too do what the manual says, minus the part about dialing the day optic up so POA=POI @ zero distance. I use a KN203, so my added height over bore is 3.75."
1. Confirm zero of day optic @ desired zero distance (100 yd for most of my guns)
2. Add SIMRAD and boresight it to impact 3.75" below your point of aim. This is a parallel zero, so your dope at all distances would need an additional 3.75" (not MOA, a fixed number of inches) accounted for. Sounds complicated but it isn't. I rough calculate it in my head (100 yd, add ~4 MOA, 200 yd ~2 MOA, 400 yd ~1 MOA, split the difference for in between distances, etc).
3. If possible, confirm windage is good further out.
4. Shoot stuff at night.
Don't mess with the height over bore in your ballistic app unless you are doing the final step of dialing the SIMRAD offset out of your day scope. Doing that definitely works well too, but I don't like what it does to my trajectory (well above zero for quite a distance).