You can go ahead and apply the SWU for all segments, providing there is no stopover > 12 hours along the way.

Each segments upgrades/clears independently. So, you may or may not get the SEA-SFO upgrade and may or may not get the SFO -HKG upgrade.

However, if the SEA-SFO segments upgrades (using the SWU) but the SFO-HKG segment does not, then you have used a SWU for just a SEA-SFO segment.

Hope this explains what you asked.

Billy