at what stage do you fit the PE

It really does depend on what the part is, I too am using PE for the first time and I've had to put a little in the model, paint the parts, then add more later at different stages. As Don said, the instructions can't be relied upon 100%. I suggest planning a rough outline of the build, I do this and it helps out a lot! Good luck!

Good question...good answers.  I've been putting off building my 350 scale ship  with a load of PE until I can figure out how and when to install it.  This helps a lot.

I remember a phrase I heard in software engineering- build a little, test a little, repeat.  To paraphrase that for PE, it is build a little, add a little PE, build a little more, etc.

It is part of the planning process, figuring out what to do when (you cannot totally rely on any kit's instructions). It is like planning when I will paint what, when.  And, it very much depends on what genre of model you are building.  For instance, most plane kits have cockpits that will be totally enclosed at some step in the build, and of course you must put in the PE before you finish the cockpit.

On ships, there is little internal detail.  When I first started putting PE on ships, I tried to hold off and do all PE as an almost last step.  Didn't work real well.  PE that went, for instance near center of superstructure involved getting past bird cages of rigging.  I do railings on ship as last steps but for the other PE it takes planning just like aircraft PE.  Now, regardless of the genre, I do this planning step before I do any building, and mark up instruction sheet as to when I add specific PE parts.

Man, you really HAVE to put the PE in where the directions tell you to. In a lot of cases, you have to shave off parts and/or replace them when you add the PE. And the PE needs to be painted with the model after being primed. Like Rob said; I can't imagine adding it AFTER painting or assembly.

Some pieces need to be put in at the same time you would put in the part it replaces (a brake and a gas pedal comes to mind). I can't imagine trying to figure out how to put PE into a completed model beyond a handful of external detail parts.

Depends,you need to find that balance where you don't destroy the PE every time you pick up the model and trying to put it on after stuff has been painted already

I don't think there is a right answer.  I think it depends on how fragile the attachments are and where the parts are going to be attached i.e. will they be difficult to reach once the model is assembled.