I would suggest using the MegaWizard, and using the recommended flow of just instantiating the created file(I've seen people use the Megawizard to create something like a PLL, then rip the primitive instantiation out of the megafunction and put it into their file. This is ugly because it creates something that can't be re-edited/analyzed/updated with the megawizard, and usually has a bunch of parameters the user starts mucking with yet doesn't understand them).
My experience is that a lot of Xilinx designers use the low-level primitives and Altera designers use the high-level megafunctions(which in many cases, like a PLL or altsyncram, aren't that high-level). You could probably get a good message board of people going back and forth on it. I don't like the Xilinx methodology because you often end up spending too much time figuring out low-level parameters or ports to do a high-level function, and the final instantiation doesn't make any sense to a casual observer(where a megafunction can be re-opened and is usually pretty clear.) That being said, there are times when you want to know the low-level details and have trouble figuring it out in the megafunction. The Xilinx DSP blocks are a good case, where I've seen people basically put in op-codes to do something like a multiply-add. There was no way to figure out what it was doing without going to the datasheet and finding this op-code, so for the general case it was painful. But for someone who is changing those op-codes on the fly and doing some funky stuff with it, it was pretty cool.
You'll also find Altera's low-leve primitive documentation isn't the best, while their megafunctions are usually quite good(and Xilinx tends to be the opposite, although I haven't looked in a while, and there are always cases that these aren't true). Altera's documentation is more the device handbook, which describes the PLL, the DSP block, the memory blocks, etc., and then the megafunctions are used to access those blocks.
Anyway, that's just my feeling, but hope it helps. (Not sure if I really answered your question rather than wax philosophical...)