Remember that before computers there were IBM punched-card tabulating machines (widely available and sophisticated by the mid-1930s and perfect for this kind of work) and these were extensively used to prepare telephone bills. The tab machines remained in use to supplement electronic computers well into the 1970s (a punched card was included with the bill that you returned with your payment). Before tab machines there were accounting machines (kind of a supersized cash register); so in larger areas bills were automated for years. I presume in small areas they either used the facilities of large cities or did bills by hand.
Keep in mind that before the 1960s toll calls were expensive and people made a lot fewer of them. Making a toll call was serious business back then. So, undoubtedly many subscribers had no toll charges at all and the phone bill was much simpler. I would not want to be a clerk doing nothing but hand-figuring every telephone bill all day long, but back in the 1950s and earlier a great many people were employed doing just that in all kinds of industries.
In cities, message units were used to tally up local and suburban calls. There was a meter attached to each line which would increment for calls and time of call. The meters were photographed and the values processed and a single amount transferred to the bill. The use of message units instead of itemized billing saved considerable paperwork.
In Los Angeles, they used itemized billing and in the 1940s they developed ANI (auto number ID) and a crude AMA (auto message accounting). Tapes were printed of call activity.
In the 1950s they developed sophisticated AMA that prepared punched tapes which could be processed by machine.
Surprisingly, there was less standardization in bill preparation across the Bell System than I would expect. Bills in different places had different formats in the 1960s. Different places used different kinds of computers -- some Univac, some IBM. Although Bell Labs developed many computer systems for the business office, it appeared billing software was programmed independently. Some billing formats may have been mandated by individual state PUCs so variation had to be allowed for that.
By the way, very recently the New York Times had a story on complex phone bills and ridiculous charges they add in.