1) create a new item - non-inventory or service item will work  - have it coded to show up in your income account. If you think its truly non-taxable to your customers, then set that "shipping/handling" item up as non-taxable. This will separate it out on your sales tax liability report. Now your shipping income will not be included as taxable sales on your liability report. 

When you pay shipping expenses, simply code those to expenses or COGS depending on nature of your business. If you need to see the difference between what you made in shipping fee income vs. shipping fees expense. Run a "quick report" under the items list, chose the "shipping/handling" you created. run your date range. You could create a special income account and a special item just for shipping income, but I think that is unneccsary to see on a Profit and Loss. If you consistently use the invoice item, then you can run a report by any invoice item. Make sure to account for cash or accrual when running those reports as well.