Hi Paul. Forgive long winded reply. From my limited experience I have found it depends on the stock to be converted, and bare in mind I'm new to this so please bare with a big pinch of salt, and it is simply the way I have done it "so far", and not necessarily the best, a right or wrong method.
On some Bachmann BR wagons that were already plain grey or plain brown, all I had to do was spray the under frames with sleeper grime (no black chassis allowed), apply CIE broken wheel or flying snail decals using 'decal fix' which helps with matt finishes, and then gently weather the wagon bodies (sleeper grime for the grey wagons, frame dirt for the brown wagons), finishing with a coat of humbrol matt varnish from a rattle can. I now always remove the wheels first but that only takes a few seconds, but before that to avoid removing wheels, I used to plug a small paper template with slots between the wheels and under frame sides (i.e. to avoid spraying the wheel surfaces and generating future track dirt). Another reason I now remove the wheels is to hand paint the sides of them with sleeper grime (i.e. to get rid of the metal or black finish on RTR wagon wheels).
Other wagons and coaches I have simply sprayed Halfords plastic grey primer on them without removing factory paint, and then resprayed in desired colour, light weathering, decals on matt surface, and then matt varnish to seal. In some cases I have rubbed off protruding factory logos and thick lining using ultra fine sand paper before priming. Halfords is wonderful and can hide a multitude of sins.
On the two recent locos, for decals I played safe with convention, and applied gloss varnish after weathering, then applied the decals to the gloss surface, and the finished with matt varnish to seal and get the dull matt look back. Decals seem more prominent and numerous on locos and I like the way they appear seamless when applied onto a gloss finish which can be brought back to a matt or satin finish (i.e. no visible edges to the transfers nor colour variation). Hope that makes sense. Noel