Hondata

I have my fan connected to ACC power because i have a bad temp sensor. Now if i was to use the "override radiator fan control" option in s300, would this mean i could put the fan back to stock and not need the temp sensor?

ECU works in parallel to the fan temp switch(or sensor as u call it),so as long as one is working correctly,then u will be fine.
Its nice to have both working correctly as a sort of fail safe though.

U will need the fan control wire correctly wired to the ECU,which in a 2000 teg(from your sig) i'd assume it would already be wired correct.
If it doesnt work,then suspect the wire is missing.

Dont forget to use a relay to control fan via ECU,dont control it directly off the ECU,the load is too large.

when you say "either one is working properly, you mean the temp switch and/or the ecu right?

Also the fan relay in the fuse box is working correctly so i should be ok right?

yes,switch &/or ECU

i mentioned the relay because i dont know how u have wired it to make the fan run temporarily off the ACC power.
So just make sure u reinstate whatever wiring changes u have made to the fan supply,to run back thru the relay in the fusebox that u mention.