Just about any sort of soft sponge or foam can be used to fill cavities such as cockpits or intakes. It's also possible to use normal tissue paper scrunched up with some water dropped on to keep it in place.
As for canopies, like John says, ready-made mask sets from companies like Eduard are probably the easiest. There are a couple of other ways:
Use wide strips of masking tape to cover the entire area you want to mask and then cut around the frames to remove the bits you want to paint. You must take great care marking where you need to cut (use a cocktail stick or biro to burnish the tape and mark the outlines), and use a fresh blade in your knife to ensure a clean cut. I've seen videos of people using a biro to mark the edges, remove the tape and cut it to shape with scissors, then replace it as you would with ready-made masks.
Use thin strips of masking tape around the edges of the frame and fill in the rest of the area either with masking tape or liquid mask. This method works better on larger areas, but it does reduce the risk of scratching the canopy that you get using the method above.
If your hand is steady enough, you can paint the frames freehand. Any paint that goes over the frame can be gently scraped away using a cocktail stick cut to a chisel shape (I guess you could paint liquid mask over the areas you want to cover, but achieving a neat, straight edge would be really difficult given the rubbery nature of the paint).
There are lots of videos showing all these methods in practice, but like lots of things in modelling, you might want to try the various options and pick the one that works best for you personally.