Motion 5 - tracking/masking question

You can simply tur the layer off and then back on a few frames later by keyframng transparency. This is usually adequate for the illusion you are trying to accomplish. If your foreground action is slow enough, though, blinking the bullet hole off and on may not sell the effect and you will need to use an animated mask to profressively hide and then reveal the hole as the foregound passes.

Not difficult but tricky the first few times you try it. Practice in a copy of the main project and turn off everything you do not need while you use a masking method. There are many ways to do this. You can use an alpha layer to obscure the hole or you can add a mask shape to the comp or you can add a mask to the layer. You can also use the write-on style effects.

As David said, you can keyframe the opacity. I'd use the "Constant" interplation method, set the first keyframe at 100%, then go to the frame where the bullet hole needs to disappear and set the value to zero. Then go to the frame where it should re-appear and set it to 100%. Then go ot the keyframe editor ("Show in Keyframe Editor" to the right of the parameter in the inspector) and select the 3 keyframes. Right click to get the contextual menu. Go to the Interpolation options and select "Constant".

When you say the mask is white, I'm assuming you have the actually created a shape layer, not a mask. If this is the case, not to worry. Select the shape layer in the layer list, and go to the Object Menu, Towards the bottom of the menu, there will be an option to convert to mask, select that and your shape will be changed to a a mask (if you accidentally create masks instead of shapes you can use this option to reverse those). You can now drag the mask layer onto the clip you are trying to rotoscope.