Rob,
I cant answer this question directly in Canon's terms.
But generally what I know from camera and flash exposure comm is done via the camera's internal meter CPU, lens CPU and flash CPU at the same time. Each provides little bits of information relay for the final flash output.
Say in your situation at 1/60 and f/1.8. You set the manual setting for it, and will force the camera flash to compensate any light that is needed to get that exposure. Information such as lens focus distance and camera metering info is transfered to the flash and it does all the calculation for you on the final output based on the complex formulae they got inside.
On AP
mode, the camera will suggest you with the aperture and shutter that matches the 'exposure' it is needed, without flash. On the Nikon Cameras, there is an option that restricts the slowest shutter speed with flash onboard, which it will then use flash to compensate the left-over underexposre.
Back to your question, I dont really use Aperture priority in with flash anyway if I gonna leave it on Auto
mode. Manual in setting aperture and a shutter which you can hand-hold the lens is best left there and let the flash exposre itself to the right way.
Another way to correct this is increasing/decreasing in-camera exposure vs on-flash exposure, they compensate each other and will make up another exposure method.
For the actual "Manual flash" I suggest you do some readings at using GN (Guide-Number) for flash exposure calculation. Its a formula based on distance to subject, aperture vs shutter and ISO on film/sensor. I cant pull the formula out from my head now, but im sure other members can help you here and/or just google it, should give you plenty of results and good readings.
PS. Pls correct me if Im wrong.
Good luck
