Usually peak the signal close to band center on highest (south) satellite. You want to get best signal from all transponders if possible, but some sats are a little off "kilter" so sometimes you have to compromise a bit.Otherwise it should work the same as it did before the mod. Think there is an arrow that points up (or down). If it's a Chaparral the instructions ahould have a picture; should be something on-line.
Hopefully your Ku will match skew with your C-band; or maybe you can adjust Ku seperately after peaking C-band on your modded feedhorn. Depends on the probe position.