Most fittings can be attached/assembled to the deck before hand. The photo etched has to go on before painting in my opinion. I use MM enamel for the color of the ship (whatever gray), this also serves as a primer, and is airbrushed as the first thing in painting.
Next you probably want to mask and spray the hull red
Next if different colours for fittings are required you can brush paint them. That is third.
Then paint the deck wood color. You will have to touch up some of the fittings and probably some of the deck no matter how careful a painter you are .
I leave off some of the bigger fittings and superglue them on later .
I then spray the whole ship with MM flat laquer. Then I do a diluted black oil paint wash.
Then drybrush if it is needed anywhere . Last thing is to attach stretched sprue for the antenna/wires/rigging.
Use good brushes from a real art store. They aren't cheap but will last and do the best job. This will make the joint you mention from photo etch to plastic, easier to paint with a good brush.
If you ask ten people they will all do it differently, you will have to find your way through experience, as to what works for you.
Whatever you do don't rush it, or the paint from drying/curing.
Note that Tamiya acrylics are notoriously difficult to brush paint, if you haven't worked with them before. I do use their hull red as a base for most hulls, and airbrush it.
You have to have a lot of patience as a ship modeler.