The dogs: it's a matter of training, if you're hoping they'll share the same space or at least back off a bit. My most chicken aggressive dog, we've worked on her with "Leave It" and she does now peel away from the fence on command.
Or consider setting a hard rule in the household that the dogs and chickens are never to be out at the same time. If my dogs are outside, my chickens are fenced in. If the chickens are out of the run, the dogs are indoors, period.
The chicks: change is scary and upsetting. That's why they were upset when night came and they couldn't see well in this new environment.
I am also at a loss as to why they could fly and jump alllllll over the guest room but not get on the ramp to go to a safe, cozy space. What am I doing wrong? Are they too young? Am I too green? Does this just work itself out?
Nothing "natural" about a ramp - you'll need to train them to use it, either via treats or herding them physically up and down. I actually prefer steps because chickens seem to be able to use them without any real training. Also take a good look at your ramp - it could be too steep for ease of use, so reducing the angle could encourage them to use it.
Also, idk why I did not think about this when I got the chickens...but am I going to have to wake up with the sun to let them out of the upstairs part every day so that they will lay eggs eventually or will the sunlight that comes in through the little window they have be enough? I really do not think I can commit to letting them out at that time every day....more like 8 or 9 to be honest.
You can go with an automatic door, or make them wait until you get up (which I did for 2 years, then I opted for auto door). I personally am not willing to increase risk of predator attack by leaving the door open.
The only caveat is if you live in a hot climate, they can die of heat exhaustion if your coop isn't well ventilated and they can't get out to get to water quick enough in the morning, however I don't know your location or coop placement to know if that's an issue.
is it ok to just leave that open and let them do their own thing even on cold nights in the 20's?
That depends. Realistically, is the run safe enough? Is it covered? Is any opening larger than 1/2" covered? Is all the wire
safely attached (i.e. is wire is sandwiched between pieces of wood screwed into more wood, or attached to wood with screws and fender washers to prevent pull out)? Is there an apron around the entire perimeter?