How do I get billable expenses to appear at the bottom of the invoice as a group rather than appear by the date which they were entered ?

You will be able to place billable expense with subtotal after product/service items. Since billable expenses were entered as a separate item, there is no group all those billable expenses and show as one item. In order to do that, you will need to customize invoice format. Open Invoice form, click customize button at the […]

I would like to apply a percentage discount on just one item in my invoice. How can do it?

There is no way to set up a discount for a fixed amount at this time. This option for a % with subtotal is badly needed in new QuickBooks Online. I Suggest sending in your QuickBooks Online Feature Requests here: http://feedback.qbo.intuit.com/