I assume you are referring to 57/08 pickups. I don't own a PRS 12 string, but I have played several, and found them to be wonderful instruments, and I certainly wouldn't expect any problems.
Just make sure that you can get the 12 string tone you want out of it. What I mean is the HB-12 doesn't have any coil split capabilities for its' pickups (anyone correct me if I'm wrong on this), and you may find it a bit harder to get some classic 12 string jangle single coil tones from it. If you like the warmer sounds from your 12 strings, it will certainly give you that.
I have two electric 12 strings from brands that will remain nameless, one built into an old doubleneck with dual humbuckers, and the other with toaster single coils. The humbucker 12 is better for harder rock applications, and the singles do the "classic" electric 12 sound (jangle-jangle-jangle....).
You might watch out for one of the older Custom 22 12 strings, as they include a single coil between the two humbuckers and can cover a lot of different 12 string tones.