I don’t really know where else to post this topic, and in case you don’t understand, if the player clicks the screen with a tool equipped, and an animation plays, will the tool go with animation?
any answers will be appreciated as I am still learning 
Yes, the tool handle is welded to the right hand (for R15) or right arm (for R6), so it will move with either part. If you want to animate the tool itself, you’ll have to create a new Motor6D joint and remove the existing weld.
Another question, if the tool moves with the animation, does the tool still do something? for example: I have made a sword that plays with an animation when the screen is clicked, does it still do damage while moving? sorry, my wording is probably tough to understand.
Yes, the sword will still physically interact with the environment and trigger events.