If you're using FIPS codes, I would program in at least two. The first being the county where you live. The second FIPS I would assign is for the county in which the NWS office is located. (Unless they are the same.) I have found that for some reason NWS may transmit the watches only on their home county FIPS and not on my county FIPS. Warnings do come through on the local FIPS# usually. You may get a few more alerts this way, but I think its worth it not to miss the watches.
Also, TV station coverage areas may include more than one NWS coverage area. They may diplay an on screen message and it be for another part of the state issued by another NWS office.
Ditto the reminder that you can't do SAME alerts while scanning. You can do wx prority and get all alerts put out by your local NWS for all counties they cover while scanning.
If you still have questions you may PM me if you'd like.