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These are more my personal recommendations based on my own experience in VectorMotion and knowledge of its features and problems.
Because scenes works laggy unreliably in VectorMotion what you can do to help yourself (especially with a lot of layers) is it name them by one scheme. For instance when I want to denote that some objects represent a whole I do something like this:
Card 1
Card 1 / Highlight
Card 1 / Close button
...
In other words just by names it's understandable that these layers belongs to the same object they represent. Usually one layer of them doesn't contain any slash and something after. I personally treat this layer as the primary one, which denotes the whole shape of the object. In our case this is the first one which is Card 1 and contains the card background.
When it comes to animating a complicated object represented by several layers which should smoothly stop and continue moving it can be hard to make it right. Not only because ideally we could use groups, which currently is not a stable option, but also because easing can't be done precise in VectorMotion which leads to small movement inconsistencies when you look closely to the animation keyframes. Objects will be aligned nicely at the keyframes you defined, but between them their movement will be distorted a little bit (or not) and depending on the animation speed it may be noticeable or not at all (for the regular viewer).
So what to do? If during your movement all layers representing this object don't move relative to each other and don't change any properties of themselves (like transparency), you can render object and export (as an image with transparent background) when it's still and use this image representation of the object during any movements with easing applied. After and before such movements this image representation of the object can be hidden and previously mentioned layers used.
Unfortunately, you can't randomize a shape (via Displacement filter), transform this shape to a path (getting rid of the filter itself) and then apply the boolean operation itself. As a workaround you need (if made with filter) to use masks to hide that part of the shape which should have been hidden by the boolean operation itself. It may not always be an easy or good solution, as the shape you want to be eliminated may be a perfect shape like a perfect circle (which will require you to make sure that the mask itself a circle, or almost, not noticeable by a naked eye).