I use flash almost always except when shooting landscapes. Since I use radio triggers, P-TTL is not an option for me, so I always shoot with both my camera and my flashes on manual. They key thing is to remember that due to flash duration, your shutter speed means nothing to what you are lighting with flash, it's the ambient light that gets affected the most with you shutter speed, so I usually just balance it out (or eliminate it if need be; here's where I'm bummed that Pentax cameras only sync to 1/180). So let's say you want more of the ambient light to be visible in your photo, then lower your shutter speed, want to get rid of a nasty green hue from flourescent light, use a faster shutter speed to cancel that light out. This of course works wonder for those nice sunset/flash lit portraits
I for the most part set the flash to an intermediate power setting such as 1/8 power and then I will control the intensity using the aperture; if the flash is too hot, I stop down the aperture, it's underpowered I open up a bit, provided of course I don't need the extra DOF.
In case I do need the extra DOF I will do one (or a combination) of 3 things: either up the ISO, increase the power on the flash or put the flash closer to the subject (the opposite goes for when the flash is too hot and I want to keep a shallow DOF). I do this because it's easier to change settings in the camera that having to go over to the flash and change something. Also setting the flash to something like 1/8 means faster recycle, less battery drain and longer flash tube life.