PE are painted only after assembly in 99% of cases. Mostly because, paint adhersion on PE/metal is generally poor and handling (folding/cutting) will damage the paint causing rework or worse. It also helps with gluing the PE parts since you'd rather want glue on metal than glue on paint which is as strong as a bond as paint on metal, read not strong at all!
If you are a practioner of a hairy stick, it is just one of those things that are harder to do - than spray painting. Have to reach all the nooks and crannies by brush, as well as not over-applying the paint to avoid smothering the finer details.
Railing are typically same color as hull, technically some chains (horizonal bars) can be black/darker but in 1/350 scale it's not necessary to paint them.
Since you've done a ship end to end now it's time to introduce IMO a systematic way to build model ships, starting with planning.
When building a ship, depending on the color scheme, you hace to plain ahead. Unlike Aircraft (paint cockpit. assemble fuselarge, mask, paint) and Armour (assembly, paint), subassembly on ships vary depending on the color scheme. So if eg your crane is the same colour as the deck structures they are attached to, you typically glue them together then paint together. But you also need to visualise when you designing sub assemblies, that you do not over-build structures as to make subsequent painting difficult. Ie you do not want to create hard to reach spaces that needs to be a different colour unless absolutely necessary. It's tempting to build build build and see progress but often times it is counter-productive.
Basically you want to paint as much parts of 1 coat of colour in one go, call them sub-assemblies dividied by color. Usually ships has 1 or more vertical colour and another colour for the horizonatal surfaces. the sequence of which you do it depends on how easy is it to mask each colour, and most commonly, people paint ther main deck first be it wooden planks or deck blues, then mask the painted horizonatal surfaces then paint the vertical surfaces whatever colour they should be. This is simply because it is far easier to mask a relatively flat surface (horizonal surface) than trying the other way around.
Say a ship like KGV with a fairly simple scheme, I would design my process thus:
1. before installing any PE railings, I would paint the wooden deck parts and horizontal deck surfaces (darker greys) first. Why? because it's harder to mask the deck after you've installed PE, and since PE rails are to be painted the same colour as the vertical surfaces, you don't need to install them first[quote user="BBorBust"]
If you have a superstructure level that has a horizontal colour, you should not glue on the upper level that sits on the horizonatal surface - it's easier to mask a mostly flat surface of an empty deck than masking the small gaps when everything are sitting on top of it.
2. mask the various deck levels, leave gap on each deck edge where PE railings are to be installed - obvioiusly you must not stick PE on paint mask...in KGV's case, the boat deck on which the crane sits (including the base of the crane) are of a different colour so you probably want to paint the cranes seperately (light grey) then install them later.
3. Apply PE railings etcs, resist temptation to stick on any superstructure parts on hull, but keep any sub assemblies that are same colour as comopletely built as possible before painting
4. Paint the rest of the colour, and peel off masking horizontal surface masking.