First question - is your company already compliant with and/or certified to AS9001? If not, is your company compliant with and/or certified to ISO 9001:2015? There are several overlapping requirements.
If the answer is no to the previous and you plan to produce IPC Class 3 assemblies, there is a lot more work to be done than just establishing better reflow profiling skills and assessing your stencil designs, which, by the way, will go a long ways towards improving your overall quality.
That said, there are tons of white paper articles, many of which are available from SMTnet, that will help establish a robust SMT process.
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