Basically you should ignore the PHY mode unless you have problems with the drive when it's connected to a SATA 3 port. If the drive can't be recognized when attached to a SATA 3 port, use the jumper to force the speed down. It doesn't really matter whether the speed gets forced to SATA 3 or SATA 1.5Gbit/sec mode, since the drive itself can't transfer data any faster than 1.5Gbit/sec anyway.
"PUIS" means "power up in standby". It means that the drive won't spin up when power is first applied to the system - it will wait for a "power up" command from the host. This protocol is used with large arrays of drives so that they don't all try to start up at the same time - drives consume the maximum amount of power during spin-up and by staggering them the maximum power draw is reduced. For a desktop system with just a few drives you shouldn't use this jumper.