I would like to create an area on my PCB where you can write on with a pen. Is this possible, and if so how should I do it?
A common practice is to leave a square area on your PCB, filled with white silkscreen as a background. If you would like to write on the PCB with something other than a permanent felt marker (e.g. a ballpoint pen), a paper adhesive label could be placed over-top of the area.
If you use an adhesive label, make sure that it's applied after reflow/soldering.
Yes. You can write on basically any part of a PCB with a permanent marker. If you want, you can also use your silkscreen layer to provide e.g. a white background, or checkmark boxes etc.
This is pretty common, eg. for boards that go through manual QA.
If you use a sticker, make sure it doesn't go near any high voltage sections. The adhesive can break down over time and cause problems. Same goes for some inks.
If you ever decide to serialize via the board house level instead of writing manually (say, for limiting the board house's marking of their manufacturing stamp, CE marking, etc.), another option we've used is to mark out a rectangle on a mechanical layer that is labelled "Note 11 on Top Overlay", then in the design notes add an annotation that reads something like "11. Mark Vendor ID, Date Code, and UV94V-0 Using White Epoxy Ink".
Agreed on labels, the adhesive is basically made of organic compounds and can be carbonized with high voltage.
This HV breakdown problem is not just a problem for adhesives. Often times PCBs have a keepout zone used to separate low voltage from high voltage circuits. From personal experience I know that quality inspectors use either office supply stamp pads or permanent markers for their notations and usually zero in on these zones. The inks generally use carbon in their pigments and I have experienced breakdowns that forms tracking paths following the inspectors marking. if you must use these inks in critical area, you really should do insulation resistance testing on a sample or PCB coupon.
The Best practice is to provide a designated zone for notes where there are no HV circuits involved.