You put it in the Handling Charge that can be added to every Shipping and Handling fee.
For example, if you choose Calculated shipping and to your customer that would be, say, $8.56 and your Handling charge is 45 cents, your customer will see $9.01 as the shipping fee. It will not be broken down. If you use PP to print your labels, the amount you pay (which is higher than just the postage in any case considering GST and fuel surcharges) will not be seen by the buyer.
In my opinion, it is not a good idea to offer too many alternatives. If you want to protect yourself with insurance or tracking, charge everyone for it. Don't give the customer other alternatives. They will want the lower price and expect the higher level of protection. And remember that the one protected by insurance and tracking is the seller. The buyer is protected by using Paypal.
And if it really bugs you that the buyer is paying "too much", an amount he agreed to when he bid, btw, then you can refund him. Remember to reduce the refund by the 9% eBay s&h fee.