I usually pay by bank transfer to the account details on the invoice. When asked to pay a deposit, I have spoken to someone at head office and given them my card details, just like I do if buying something over the phone. I then get a receipt either from the salesman/estimator while he’s with me via email.
I don’t worry about paying this way, I tend to use reputable companies based on recommendations from friends or local community groups. If I am using a company for the first time, I might research them online, check out their website and read reviews.