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The customer pays you a price inclusive of VAT if you are VAT registered. You should account for that as VAT output in your accounts and VAT returns.
The charges (fees) from Amazon for the service may or may not have VAT charged on it. In the event there is VAT charged to you then you claim it as VAT input in your books of account and VAT returns.
You have to treat these as two separate transactions notwithstanding the fact you receive the net amount from Amazon/ebay after their fees has been deucted from total sale value.
VAT on delivery charges -
If delivery is free or the cost of delivery is built into the normal selling price, then VAT is accounted for in the normal way i.e on the total invoice value.
Normally, you would charge VAT on shipping charges if you are VAT registered.
For better understanding of VAT treatment under different circumstances, please look at sec 2 and 3 of VAT Notice 700/24 (April 2003) here
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