Yes you can use the save function aswell. You just have to set the instance variable (or animation frame <img src="{SMILIES_PATH}/icon_e_smile.gif" alt=":)" title="Smile">) of the object and then save the whole game state.
If you use the save/load function you don't need to do that though, because it will save the whole state of the game.
Here is an example capx with a working waypoint system:
https://drive.google.com/file/d/0B7r2WY ... sp=sharing
In my example you actually don't even need to use an instance variable. I just used the animation frame of the object (You can have an activated animation frame and a deactivated one). 0 is deactivated and 1 is activated.
I hope this helps! <img src="{SMILIES_PATH}/icon_e_biggrin.gif" alt=":D" title="Very Happy">