You can use ordinary pads instead of conductive shapes.
For example consider a GND net is having thermal pad. Then you can create pad for particular(GND) net including that thermal pad
(Resultant pad size = ordinary pad size + thermal pad size).
By using this method you won't worry about mask openings and other things. Because you already define mask opening in your pad stack.
If you are using conductive shape you have to manually draw the solder mask openings.
I think this one will help you.