The relevant chapter of the limma User's Guide is Chapter 6 "Pre-Processing Two-Color Data". Chapter 12 covers the more advanced topic of single channel analysis.
For most analyses you need only the normalizeWithinArrays() step. The Aquantile normalization is only needed for single channel analysis. When normalizeBetweenArrays() is mentioned in Chapter 12, it is assumed that the normalizeWithinArrays() step has already been done. Aquantile normalization is never used by itself. If you are not doing a single channel analysis, then it will make no difference to the final results whether or not you do the normalizeBetweenArrays() step.
In summary, the normalizeWithinArrays(RG, method="loess") is what you need and usually it is all you need.
Sean Davis gave the same answer to the earlier post 4 years ago.