applied for VAT Registration

What do I during the period where I have applied for VAT Registration but I’m still awaiting my number?

My account advised that I need to start charging VAT on my sales but because I don’t yet have my number, Amazon are still charging VAT to me.

Can I upload the VAT number once I have it and request a VAT refund from amazon or will the VAT refund need to come from HMRC for that period?

Yes mate, you can charge and reclaim any VAT going back 6 months if you need to, it might even be longer than that! So start working back pulling out any expenses you had VAT on ready to ask your accountant to reclaim it