Again like many things, there will be as many solutions as modellers!
Some kits come with pre-shaped lozenge decal sections with holes in place for struts etc. This I assume (I haven't yet used such) would also help with positioning the decals, by lining up the holes with strut locations, plus the strut brackets etc can be pre-painted before applying the decals.
Whilst no way a pro, I have sometimes pre-painted the bracket areas, then trimmed the decal with a sharp blade after applying over the whole surface. Where struts appear to disappear into the wings without any brackets on the wing surface, I have punched the strut end into its location through the decal - just need to be extra careful with glue!