Hi jms,
The software will allow you to choose the character that is used to identify a new comment (for most firmwares this is a semicolor ";"). Some firmwares may require a different character, for example I believe the CubeX firmware requires a pound sign "#".
When you upload the G-Code to your printer, these comments will automatically be stripped and only the raw G-Code will be sent.
Does that help you? If not, feel free to contact our customer support staff at
support@simplify3d.com and they can provide further guidance.