Ok, here's a short tutorial on obtaining area peak factors (APFs) using boron as an example. Be aware however, that for low intensity boron peaks, e.g., boro-silicates, the background fitting is quite crucial for best accuracy.
So let's say we wanted to analyze boron nitride using boron metal as a standard. Assuming you've properly polished and coated your materials (also crucial for low energy emission lines such as oxygen, nitrogem carbon, boron, etc) and properly set up your peaking and PHA (here we peaked on our primary standard, boron metal), we then perform a high precision wavescan on both boron metal and boron nitride. In this particular run I was analyzing magnesium boride unknowns, but since boron nitride peak shapes have been measured by Bastin, we can compare our results to his measurements.

So here is a scan on boron metal:

and by clicking the Model background button we can see the background fit and by clicking the Integrate button as seen here, we get our peak and integrated intensities:

Since boron metal is our primary standard, we make a note of the Peak/Integ (St) value of 7.25. Now we plot our boron nitride sample as seen here:

Note that there is a significant peak shift in the peak of boron nitride relative to boron metal. Not surprising, but this matter for your analytical setup in that it might be better to analyze each material at it's own peak position to avoid peak *shift* effects and just correct for peak *shape* effects. We will visit this issue later.
Now we model the peak shape by again clicking the Model backgrounds button as seen here:

and this time we make a note of the Integ/peak (Un) value of 0.167 because in this particular example, boron nitride is our "unknown". Now multiplying these two numbers, we obtain an APF of 1.21 which seems a little high, especially when compared to Bastin's boron in boron nitride value of 1.20.
Ok, now you thinking "hey these are pretty close actually", but the problem is Bastin used a Pb stearate crystal which has a much higher spectral resolution compared to the PC25 multi-layer crystal I used. So really the APF for the PC25 crystal should be much closer to 1.0, so why is that?
Well it's because we have included the peak *shift* effect in our APF calculation and instead Bastin re-peaked each scan on both the boron metal and the boron nitride materials to focus on the peak shape effects only.
So, what if we re-peak our boron nitride scan for the peak intensity? But there is no need to re-run the scan, let's just re-fit the peak intensity as seen here:

How did we do that, from the Model backgrounds dialog we merely clicked the Maxima peak fit option before we clicked the Integrate button as seen here:

So now we obtain a Integ/Peak (Un) value of 0.143 and multiplying that with our original boron meta Peak/Integ (St) value of 7.25 we now get an APF of 1.036, which is much closer to what we would expect for peak *shape* effects only on a low resolution LDE crystal.
I'd be pleased to answer any questions you may have. I've also attached a write up on my magnesium boride efforts (remember you have to be logged in to see attachments!).