If you are wanting the scanner to monitor the S.A.M.E. codes for your area, the radio must be parked on the weather radio frequency. You can't continue normal scanning along with S.A.M.E. operation. If the scanner was continuing to monitor other frequencies, it likely would miss important sections of the alerts from N.O.A.A. For S.A.M.E. monitoring, your best bet is a dedicated weather radio, or an older scanner (even analog) that you are not actively using. I have weather radios at home. If away from home, for any length of time, such as a day trip, I generally have more than one scanner with me. If weather blows up unexpectedly, I can use one of the scanners as an impromptu weather radio.
You can continue to scan when using Weather Priority. That only checks the weather frequency every 3-4 seconds for the alert tone, which is transmitted longer than that interval. But that in turn means you'd get every weather alert issued by your forecast office, not just the ones you entered FIPS codes for. However, some people prefer not to have the brief, regular, breaks in reception when the scanner checks for an alert broadcast. Plus, many weather radio stations provide alerts for as many as eight or ten counties, including in most cases counties that are 'past' the county I'm in, a storm there being no threat to me at all.
