Boogie's suggestions are excellent. Here's another thing I like to do with a new amp:
Set all the tone controls to zero. There will probably be no (or very little) sound, since you're filtering out all of the frequencies. Start by turning the treble control up slowly, and take it to the max of its range. This will tell you the frequencies the treble control affects. Then turn that one back down, and do the same with the mids and the bass. You should get a very good "by ear" idea of the frequencies each of the controls in the tone stack operate on. It may help you dial in the amp.
As Boogie says, these are old school style amps, but they're very versatile if you make use of the volume control on the guitar to control your gain. He's right on as to how to set the amp up, and with a good guitar like a PRS whose volume and tone controls are actually designed to do something besides go to "10", you'll get the hang of it in no time.
Finally, a lot of players of PRS single channel amps simply dime the master and use the gain control the old school way. I tend to find that a bit too loud for my studio, so I start with the master about noon, set the gain control, and then re-set the master to the level at which the amp sounds best. Which as Boogie says, is usually 2-3 o'clock, though that will vary; on my HXDA 50 watt, it was sounding great by 11 o'clock on the master. My new HXDA30 needs 2-3 o'lock on the master, which is the point where the power tubes start to take over the tone and everything isn't all about the preamp tubes.
