It's the second option, Priority is only used when queueing to the same skillset.
Moreover, priority is used only when calls wait for an Idle agent.
A call "A" entering the system to xx
x:00, queued to skillset "1" w/ priority 6 and a call "B" entering to xx
x:01, queued to sks "1" w/ pty 1, if there is an Idle agent when the call "A" is queued, it will be presented to this agent and the call "B" will wait. But if both have to wait, the call "B" will be answered before "A".
If all agents have the same skillset and no priority difference, you should use only one.