You'd want to avoid metallic pigment inks and any black inks containing carbon, UNLESS there is a dedicated area to write on with no signal tracks. If you are laying out a PCB that you expect to hand-annotate, provide rectangles of white silkscreen to write on either over the groundplane or bare PCB.
Totally bare FR4 (no coper, soldermask or silkscreen) can be lightly sanded to roughen the surface and marked in pencil, and also erased. However you need to be careful to avoid conductive graphite dust getting where you don't want it.