solder mask openings are created automatically when placing pads or pins using the add pin tool. If you need to cover a pin with solder mask right click on the pin, select properties, and check the tented box.
You can create additional solder mask openings by placing a filled polygon with the appropriate size and shape on the top or bottom solder mask layer. If you created complex pad shapes or are using filled polygons as pads you must remember to create the solder mask opening as described above. Polygons on the top and bottom copper layers will be covered by solder mask unless you add filled polygons on the mask layer to create the required openings in the solder mask.
The PCB123 default solder mask view is negative. This means that each pad you see when viewing the solder mask layer is actually an opening in the solder mask. If you prefer to view solder mask as a positive view go to View > User Preferences > Display and check the Draw positive soldermask box.