what should be the balance between clerks and craftmans? what should i enoucrage? which is better?
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Clerks to Craftsmen ratio should be 1:5 so you will get more throughput, but in... late mid game... factories will run good even without them, if you research techs well.
PS. Clerks give you RP points. If you have 4% in whole country you get full bonus. But the clergy is much more important.
Actually the ratio is 1:4 not 1:5 as you want 80% craftsmen and 20% clerks.