I don't think you can customize the size of the work units. But what I can tell you is that my PC is not a dedicated/unattended rig and I don't leave it on over night so I need some control over the folding. In the
Advanced control tool, there is that very nice feature: the "Finish" button. When you click it it doesn't stop the folding but makes sure no WU is requested after the current one; this even works when the slot is requesting a WU but didn't get it yet i.e. the GPU slot is requested but no WU is available so if you click "Finish" in that state it will still take one when one is available but will stop folding after it's done. I think you can pass --finish to Fahclient.exe (see fahclient --help).
What I do is that I start folding early in the day and apply "Finish" then when the folding is done I evaluate if I have enough time in the day for other WUs. It's always a gamble as some WU could be longer (i.e. I have had some CPU WU last 24 hrs or GPU ones with 8-12 hrs). I imagine using the
Task Scheduler and passing the "Finish" argument to the CLI with the account you want, this works if you accept you won't be able to choose the size/duration (generally it goes against policy to try to
manipulate the assignment servers).