do they thoroughly clean up after themselves in the yard, or do they just kind of grab the main things? Do I have to steel myself for losing some plants?
You should consider having a cleanup clause in your contract or description of works document.
Ie acme roofing company warrant to leave the yard and environs in similar condition to prior to start date. Take photos of your yard and house prior to work starting.
Ask where they will dispose of surplus products. Is this a legal disposal point? Is paint invoved? where will brushes and rollers be cleaned. paint down the drains is not good and even less so out in the street.
Ask the company about plants. It may be easier to dig them up or cut them well back and get them out of the way.
Remember everything that happens during the job is your responsibility unless the contractor accepts responsibility in writing.
as we dont have asphalt type of roofing here in Aust. i googled and came up with this site.
I'd recommend a thorough study of all the pages and links you will then be able to ask questions which make it sound like you know all about the job.