A few thoughts -
I can't see it being in anyone's interest to make freeware software for this available. Some of the sets of schedules software out there are modular, in that you can have a basic version with limited functionality.
Doing it entirely on paper or in Excel would get the basics done, and you can still do registrations and variations with hand-written timetables and maps if you want to, but at some point it's all got to go in to electronic format for BODS (Bus Open Data Service), real time systems and to be fed in to ticket machines (again, I think it's pretty much compulsory to use electronic ticket machines now.) There are organisations out there who will act as agents for this for small operators.
Having to enter all the data separately to several different systems is not only time consuming, but risks errors transcribing the data from one to another, or of versions getting out of step when there's a service change.
I've done scheduling both professionally and for a few medium sized heritage bus 'running day' events - the latter have been on paper / Excel, and it's easy enough to set up templates for timetables that are good enough for printing / PDF, individual crew duty sheets, and something for a controller.
Again, using one set of data for everything is key and copy-pasting it is better than re-typing things (if you haven't met it, the 'paste special - transpose' command will copy a horizontal row and paste it as a vertical column, which is occasionally useful.)
But it's worth checking and re-checking to make sure that the vehicle workings and crew duties all make sense (sort by duty number then by bus running number and you can set up a simple calculation to show layover times - if anything comes up with a minus number you've done it wrong!) and that every journey on the timetable has a bus and a crew / driver.
Traditionally it was done on bespoke graph paper, with time along the horizontal axis and buses and / or crews on the vertical axis. Somewhere I have a sheet or two of National Bus Company scheduling graph paper which I acquired when I was at my first job in the industry and shown the basics of scheduling. Again, this is fairly good for showing overlaps or gaps.
Getting Excel to show this is possible, but long winded, and it won't do it automatically.
There's some simple examples shown on this
web page.
There's also some live London Transport bus schedules office action in the British Transport Films 'All That Mighty Heart' (1962/3) at around 12.30 to 12.50 (link to Youtube
here) - the man drawing diagonal lines on a graph at 12.50 appears to be adding crew duties to a graph that's already got bus workings shown on it.