Stages 3, 4, and 5 can be configured for either heating or cooling. Do this through the Configuration menu. See the user manual for step-by-step instructions.
Yes, there is the option to have ventilation off and only heat stages active. This is most often used when a room is empty and only needs to be kept from freezing. It also has multiple programs that you can use for different seasons or scenarios.
No, the two variable stages are for cooling only. The three relay stages can control either cooling or heating. The Plus-Touch can control variable heaters.
The only stage with proportional heat/cooling control is stage 5. Technically you could wire one of your variable fans in series with stage 5 so it intermittently disconnected the source voltage as the setpoint calls for it.