The hops and other “stuff” that rise are normal, it is called the Krausen. It happens during active fermentation and no need to worry about it.
And yes, you want to stir in the hops during the boil. I don’t know all the scientific stuff that happens, but boiling the hops is how many of the yummy oils get worked into the wort.
So since most of the hops stuck to the sides of the pot at boil, is there anything I can do or am I overanalyzing it? I just don’t see the hops in the Honey Brown that I do in the Petite Saison.
Did they stick to the sides near the end as you lost volume to evaporation? Or for the whole time? If just near the end, then I don’t think it would be noticeable.
Honestly, I would not worry to much about it. Worst case, it will be a little extra malty and slightly sweet. Totally drinkable though! I like my browns kinda sweet.