Are the fee's included in the transaction with the other trade sites? or does the 0.3% fee (for example) get added after?
They occur at the same time as the trade transaction. Some exchanges list them as separate transactions in the history, and others include a fee column but all exchanges charge the fee when the trade is made.
Some exchanges subtract the fee from the proceeds of the trade. For example if buying 1 BTC at $10 and there is a 0.3% fee, you will be charged $10 but will only receive 0.997 BTC.
Others add the fee to the purchase price. For example, to buy 1 BTC at $10, the amount charged is $10.03. The fixed-rate exchanges would normally be the ones that function this way.
