yes, go ahead and book the AT now, if you can. Prices will most likely only go up from there. If they do go down, you can call Amtrak and have them put the cheaper price on your tickets.
Yes, they are refundable up until either one week or day of ... I keep forgetting which, but it should be on-line or someone else on here will let you know.
We were in DC the other day and gas was $5.35/gallon

Around here it is $4-$4.10/gallon (or Costco/Sam's Club under $4). Another reason to purchase your tickets now, in case AT decides to raise their prices to cover future rising gas costs.
You can see a whole lot more from the upper level and that is where the lounge car and dining cars are. The upper level feels more open (IMO) and if there are other kids it's great for your kids to play together. At 9pm the train lights will dim and it's generally accepted that voices are quieter as everyone knows the kids are trying to sleep. People will walk through your car more, but that also provides more "entertainment" along the way - hehe.
Lower level is mostly elderly or people w/o kids or older kids. View is not as good but it's generally quieter -- except for old people shouting b/c they can't hear each other

. It doesn't seat as many so less people. You can spend your time in the lounge car/dining car looking out anyway at the upper level, so it's not like you can't see everything on the upper level at all on your trip.
We do the family rooms which are on the lower level but seem to spend most of our time in the lounge car and dining car anyway b/c we enjoy the view more up on top.