We are currently doing a lot of work on the quote feature and as a first step you can now choose the order of your favorites in the account settings page which will be reflected when you generate a new quote on a project.
So you can now order you line items from the start of the job to the finish and every time you generate a quote it will automatically appear just how you like it.
This is step one in a big project we are working on to make the quoting feature a lot more robust so keep an eye out for announcements and feel free to let us know what you want added to this feature.