Biggest challenges?
Short and simply: Not knowing where to look for the answers, and much later realizing I didn't even know all the questions I should be asking.
When my son crossed over, the idea that he could join any Troop was foreign to me. His Cub Scout Pack was a feeder for his current Troop. Same CO. As a youth I was in the same position, so I thought his progression was proper simply because it mirrored mine. So, right from the start, I lacked knowledge. I've since tried to sponge as much information as I can. This forum has been a huge part of that absorption. Other Scouters, books, magazines, websites, etc have helped me immensely.
As I've learned, I've changed my approach. Once example:
At the end of a Troop campout, the SPL lines the boys up, spreads them out, and tells them where they're to look for trash. After 10 yards I tell three shoulder-to-shoulder boys to "spread-out so your search is more effective." At the time I thought I was doing the right thing. These days I've learned to sit back keep my mouth shut and let the SPL handle the situation.
Again, lack of knowledge had been my biggest challenge.