I treat small stencil decals just the same as bigger decals. If the finish is matt and I need a gloss coat, I do the gloss coating for all areas at the same time. Frequently I do the decaling surface by surface, doing both large and small decals on that surface before moving to another area. I then either gloss coat or dullcoat, whichever is called for, when all decaling is done.
Of course, there are always exceptions. Instrument panel decals and such are put on long before the model is assembled and hence before other decals. Decals that go on subassemblies that are mostly buried during construction have to be done before inserting that assembly, to make it easy to access the surface the decals will be applied to.