I like to see squeeze out everywhere
. I figure if I haven't "wasted" half the caulk, I haven't done the right job
You could wait and see, or, while you're at it, just take the window back out and do it again.
On the awning
.... is it an awning
track? Or is the awning screwed directly to the trailer?
And is it screws for sure, or rivets?
Can you see the back? I mean, are there nuts and washers -- or did someone maybe use self-tapping screws into the fiberglass. If the latter, that is usually not a good plan, and I would probably want to improve the attachment.
If it is machine screws and nuts, and they aren't leaking because of any obvious movement, hole elongation, or etc., then I would remove them, wrap the top of the threads and under the head with butyl (or use caulk in which case I would tape off the trailer), and then refasten. The idea is like with the windows in that you want the sealant under the "flange," not on top of it.
If rivets, then you have to have a dollop on the top, because of the built in hole.
Can you please post photos? That would sure help in visualizing and giving our opinions on solutions.