Hi vmk0102 ,
ATUM free doesn't interfere with how WooCommerce Orders work, so you should get a POS compatible with WooCommerce, but if you are planning to use any of our premium add-ons, then only 100% ATUM compatible is the POS module we include in our ATUM app, which is on the beta staging. We plan to release it later this year.
Regarding your other question, you can track damages or any kind of stock incidence with the Inventory Logs module.
Hope this helps,
José Andrés