If you're going to remove the potatoes from the pan, you need to be careful about how you store them.
If they're just thrown into a bowl and left there, they'll sit there and steam, possibly softening the crust that you worked to develop. You can avoid this by spreading them out on a baking sheet, or a wire rack, but you instead have the problem of them cooking off too much.
Personally, I go with something closer to your #2.
- I start with par-cooked potatoes (I make extra baked potatoes, let them cool, then put 'em in the fridge), cut into slabs. and coated in oil.
- When I have a good crust on one side, I flip the potatoes over, and get a crust on the second side, and add the onion (cut into thick rings) and peppers (cut into strips, laid on their cut side).
- When the onions have good color, I flip them over.
- When the peppers have good color, I flip them over.
- When the potatoes have gotten a good crust, I use my metal spatula to cut them into chunks (directly in the pan).
- When the onions and peppers have good color on both sides, I use my spatula to cut them into more bite-sized pieces.
- I stir the whole things together, adjust seasoning, and let cook through for another minute or so.
Possibly significant points:
- I use a griddle, so there's less chance of collecting stem. (it's a 12" round cast iron griddle, which is just right for 1 potato + 1/2 an onion + 1/2 a bell pepper)
- I'm starting with a cold potato and a pre-heated griddle.
- I've done this a lot, so I know how thick I need to cut my onions (into 4 slices for a medium), about 1/2" (1.25cm) for the peppers) for the doneness I like and the cooking time.**
- Leaving things in slabs gives me less surface area on the food, but more hot spots on the pan (for better evaporation of any liquid)
- Leaving the onion in a slab ensures better contact with the pan and faster cooking. (you also don't lose heat to evaporation)
** a note on the cooking times : I have absolutely no idea. Basically, my bedroom and bathroom are right next to the kitchen, so my process is :
- start the pan pre-heating
- start the shower heating
- toss on the potatoes
- take a shower
- flip the potatoes, add onions & peppers
- get dressed
- flip the onions & peppers
- shave or quickly check e-mail
- cut everything up, (optional : scramble in a couple of eggs), season & finish cooking.