For on/off map I usually use the GM layer (with advanced shortcuts enabled to use L+O/K hotkeys) or add a DL border around one or more edges of the map to store tokens behind without switching layers. Since your animated tokens are large area, though, the former may be distracting to you and the latter may not be practical. For the Wizard Tower, I suppose technically you could make a multi-sided (rollable table) token with a static image of the intact tower and then change the side to the animated collapse and possibly a static image of the tower after collapse. For an effect that springs from nowhere, one of the sides could be a transparent png (just put a gm-only aura on it so you can find it!). You'll just have to play around with what feels the least intrusive for the specific map & token combinations you are using. Looks like you've got a Plus sub, but if you happen to be a promoted gm on a Pro game there are api scripts that can help (like SpawnDefaultToken for getting tokens to the map or token-mod for changing sides from a macro or chat menu, etc.). However, animated tokens and the api have never played nicely so even this might not be helpful in your situation.
