How do I Add a second collision polygon for attacking only

I just want it so the polygons on my character don't mess up the movement when attack like a collision mask.

You don't

Instead add extra point/points where you would want this polygon, then create a simple square sprite and attach to this point/points. You can check for collisions against those

You can also check how it's done in the Kiwi Story template. There are two sprites - an invisible Player_Base with simple collision mask and Platform behavior, and Player_Mask with all animations.