I often use a dry-wipe marker pen with a fairly sharp tip. The advantage is that it any traces of the marker can then be polished-off easily. A permanent ink marker, like a 'Sharpie' pen, can be a little harder to clean away

If more precision is required, then you could use something like a scribe or compass point to scratch the lines in, but this leave little room for error in terms of slipping and scratching the part surface

When pulling multiple parts from the same mould, I tend to lightly score the gel coat around the edge of part already cut to size and this will leave ready-made cut lines on subsequent parts