Click on the build praefecture button. Instead of left 
clicking on a grass tile to build a praefecture, right 
click on a tile occupied by a house to infect that house 
with disease.

William K'Dathi

Press 'A' on City or Province mode to accelerate time.

Nate Roberts

If your farms and/or trading posts are doing very well or there is more than one product coming into them then you can add more warehouses to store surplus or other types of products.