Ive got a few more feet of neoprene, so if I need to pad more I can 
First I would pad the whole bottom of the battery instead of 4 squares because the impacts could harm your battery if you do it like that.
How much space is underneath, above and on the sides? Best is to add as much padding as possible until every gap is closed and your battery can’t move, should be like a glove. Also you could use additional some softer foam which gets a bit compressed when closing the box.
Thank you! The screws under the foam creates an uneven surface, what would you recommend to fix that, just add foam until i cant tell its changing elevation?
Ok now I see the screws 
It depends how much space is left on the bottom of your box. If you have enough space I would pad everything except the screw area until it’s the same level, then put some 1mm rubber or silicone on the screws and add more padding.
If you don’t have enough space you could try it with shorter screws or nuts, is it bolted through the deck from bottom or with threaded inserts? I bolted my case from bottom with M4 screws and only 2mm high square nuts with thread locker, holds well. Between deck and case I put rubber washers, very useful. On bottom of my battery I have 2mm neoprene foam plus 10mm softer foam. The problem with softer foam is that it needs to be replaced from time to time because it shrinks due to weight of battery. But also on my old lipo the 3mm high dense foam was totally done after 3 months of use. Needs some checks from time to time.
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