What most people mean when they ask, "what is the best way of running SPC…" on most any process is, "what is the most practical way?" This is because SPC math demands a lot from a process.
In fact many SPC tools, like GR&R, cannot be done for a reflow solder thermal process. This is because the GR&R study demands you measure the same "part" more than once.
People assume this means you run the reflow solder profile a second time, which does NOT measure the same part a second time, it produces a second and completely new part, which is not the same as measuring the same part two times. See more discussion on this in my blog.
SPC also demands a lot of data, and even the simplest profiling tools take a little time and discipline to perform. So there is often too little data to allow SPC to really work correctly.
However, corporations willing to take the time to get the needed data from their reflow process will gain much in improved process control, proof that your oven is in control, increased yields, reduced scrap, as well as a marketable differentiator over your competition, in that it shows that you are concerned about your thermal processes.
The most practical way to collect data about your reflow oven, and thus begin to produce meaningful process SPC, is via tools which are designed to measure your oven's capability at a given recipe (oven settings).
These tools have the advantage of remaining stable over many 1000s of uses and thus allow you to see how your oven is performing over time. Unlike the original circuit board, which was used to develop the oven recipe, these tools can confirm that the oven is repeating the same thermal environment long into the future.
They can be use to check if your oven is ready to run at a production recipe at each shift change, every day, after each recipe change, etc, and at the same time capture valuable data which can be used to produce the SPC control and capability charts for the reflow oven.
There are several of these tools to choose from, like the OvenRIDER by ECD. Much more information than can be included here can be found in my blog on this very question of SPC for reflow ovens (Oven Verification) using an OvenRIDER. Please feel free to take a look.