Can you incorporate *important* ingredients after the bread has risen....some?
Hello! I'm new to breadbaking, and I'm confused. I followed the SourDo Lady's starter and basic bread instruction, and my bread tastes awesome and the crumb seems ok, but it's spreading and not rising enough for my liking. Based on what I've read here, I think I'm messing up the fermentation time, flour protein level, or my oven temp is off as I'm waiting for a thermometer to arrive. As I'm in an new country, I also have no idea about the flours I'm using (harina integral mixed with tipo 000). It's a fun mess and I want to eliminate one variable at a time. There are a lot of unknowns and future experiments in perfection waiting, but I'm pretty happy that the bread is gobbled up by my testers. I want to get the rise to improve so that I can try this one with more ingredients! http://www.thefreshloaf.com/node/12819/potatonut-bread-south-tyrol-thanks-salome 
However, I'm confused about a few things:
1. What is the difference between refrigerating dough over night with one stretch and fold vs. stretch and fold immediately 3x for 45 min, then refrigerating?
2. I keep forgetting to incorporate the butter/salt/sugar in a timely fashion. What happens to the gluten if I'm adding butter/salt/sugar in after it's risen 1-2 times? What happens if I added nuts or seeds at this points, since most recipes seem to want a first rise without that stuff? I don't really understand the rise of breads with mixing stuff in, or even if you're supposed to poke air out, then put it in the oven. See next question.
3. I accidentally collapsed my friends yeast based dough - she had let it rise twice. So, I did a few stretch and folds, and stuck it next to the other one in the oven. Her previously risen bread stayed inert when baked. The one I reformed started much smaller and grew almost to the same size as the other. How does that happen?!?!
Thank you so much for any tips!
Jessica in Buenos Aires