Weathering after decals?

You can't get weathering underneath the decals. But you can weather over the decals.

Weathering after decals is just fine, you don't need to weather under them. Consider that in the real thing a newly-built a/c would have its markings applied in the finishing stages, so any wear and tear in active service would appear over the paint surface and markings. Only case I can think of where you would want the weathering to appear under the decals is when you'd want to replicate the look of a well-worn-out a/c with freshly-painted, possibly field-applied, markings.