The "brain" in your furnace won't know the difference, a closing contact, whether a manual selector switch or a thermostat, will send the same message; Turn Fan On.
If your not 100% confident about your wiring skills then my advice to you is to take your time, sketch your idea out, add wire colours, terminal numbers and any other information you find. Most furnaces have a wiring or connection diagram pasted somewhere in the cabinet, you should be able to cipher out the fan switch connections. Use a muli meter to verify the operation of your thermostat, experiment with the components. And probably the most important thing, disconnect the power from the furnace before you start wiring, and don't repower until all your connections are complete and safety covers are back in place. Most furnace control circuits are low voltage 24VAC, and most suitable thermostats are designed for this voltage- do not attempt to run the fan power circuit through the thermostat.
Hope this is helpful!
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