Mask the cockpit or mask the canopy?

This is a brilliant question as I'm kinda new also.  I have 5 models under my belt and I'm finding the canopy in place works best for me.  I usually display my models with canopy open so if the kit has the one piece closed canopy I'll use that for the mask.  I use white glue that dries clear for application.  Only thing I hate about this method is taking of the glue residue if I need to remove the canopy.  On my current build I'm going to try thin pieces of masking tape on the canopy sills.

I'm really intrested to learn how other guys do this.

I always mask the canopy, inside and out, and then paint the inside of the canopy frame with whatever color is appropriate for the interior of the aircraft I'm modeling.  Don't use primer on the inside, because it will show through to the outside edges of the frame.  After that, at some point I will attach the still-masked canopy to the model (usually temporarily with a thin snake of Blue Tack to stick it in place AND keep atomized paint from sneaking inside the cockpit and fouling all of the intricate detail).  Then my primer goes on the whole model, including the outside of the canopy.  All of my final fine-tuning of seams and panel lines is then done, before another thin coat of primer (mostly just to the areas I fine-tuned to confirm the job is complete).  Then the paint/camo pattern/counter-shading goes on.  Then clear-coating, decaling, Flory wash, final clear coat, etc...then the temporarily mounted canopy comes off and gets unmasked.  I attach the canopy parts to the fuselage and/or canopy rails using clear epoxy.

As far as what to use for masking the canopy goes, I use tape or Tamiya masking sheet material along the edges of the frame for a sharp edge and then fill in the larger areas with liquid mask.  If you put your primer and paint on nice and thin, you shouldn't have any trouble with paint chipping along the edges when you remove the mask after the paint has dried all that time.  Just airbrush your paint either completely perpendicular to the masking line or angled toward the non-masked areas.  Don't point the airbrush at the edge of the masking, or paint can build up along the edge and can bleed underneath.  Doing it that way and building a ridge can also lead to chipping when you remove the mask.

Since I am now on my 5th model since my almost 25 year hiatus from building, and my 4th was an F-16CJ, I have no experience with getting a nice smooth transition between the fuselage and a front windscreen.  But, for that on my Su-25, I think I'll be using Milliput.  Its a two part epoxy-type putty that can easily be smoothed flush with a damp Q-Tip before it cures and has a nice, long working time.  No solvents, so it won't craze the clear plastic, and I shouldn't need to get sandpaper anywhere near it.

Here's a fairly-decent pic of the finished F-16CJ canopy.  Used the same method (with pre-cut Eduard masking sheets and liquid mask) to get the rubber strip around the canopy.

I use a strip painter tape on the inside before airbrushing, and mask the outside around the frames - depending on the aircraft. I never buy canopy masks because you use them once and toss, A huge waste of $$$ to be honest. It's not that hard to make your own mask. All you need is Frog yellow painter tape and a fresh blade. Go slow when cutting your tape on canopies.

Most aircraft models, 1/48 or smaller, have tiny cockpits that you can't see into when it's all closed up.  I don't bother painting the meticulous details in the cockpit.  I spray the inside of the canopy with clear smoke laquer, and let it go at that.  Others I know, spray opaque blue. 

If you have a closed canopy then to me it makes set to attach it, mask and paint. that way you can fill any gaps. Most of my canopy's are open, so i tend to attach the fixed parts, usually the front, mask that and stuff the pit with tissue. The open part of the canopy i wioll mask and paint and attach at the end.

Despite building mostly in 72nd, i do feel its worth detailing the cockpits, even on somthing as small as a Bf 109, and i tend to use PE. So i leave out small parts such as levers and add them at the end so they are not knocked off by the tissue.

That is a decision I make when approaching the point of mounting the canopy.  Do I want it open or closed in final display?  How fragile is stuff in the cockpit?  How complex is the canopy?  Birdcage canopies are hard to mask so I do them off the model.

If I am going to "mask" the cockpit I stuff it full of tissue ( like Kleenex).  When finished stuffing I gently wet the top layer to help hold it in place and not fuzz out.

If I am masking the canopy on the model, I often brush paint neccessary parts.  And I often mask one section or piece at a time.  Takes longer but I get a better job.