You can define code snippets in Sheetcam to achieve what you want for holes. User SeanP on the plasma spider forum had a quite a good methodology.
QTplasmac also has basic hole settings you could experiment with. Refer the QTplasmac docs.
For much more sophisticated hole processing, you could play with monokrom. It removes all hole cutting code and replaces it with its own based on a data base driven approach in terms of material thickness and hole radius. There is a video describing the algorithm on my MrRodW YouTube channel.
