Hi Erica,
As far as your first question, it depends if you just use the email from another program, or if you're dropping the campaign into the stream. If it's just the email, then that's all they'll receive. If it's the campaign, then as long as they meet the smart list criteria, the whole campaign will occur.
For content, I would do a little bit of both things that you've described... One of the great things about engagement programs is that they're smart enough to not send the same exact email to a person more than once. But if you clone an email into multiple programs (even if you don't make any changes to the email, it's now a separate email), then there's the chance that they could receive an email that looks the same as another that they've previously received. For this reason, I like to keep any nurture emails as global assets in the Design Studio, so that we always reference the correct email. If you want to track the forms/landing pages for performance and then follow up for filling out the form, this would be where I'd have separate programs (most likely built outside of the engagement stream, but could depend on your setup).
When using nested programs, you're essentially saying that two things could run concurrently... An example of this might be a webinar campaign within an engagement stream. So if you have a program with an email in 2 weeks that someone has qualified for within your stream, as well as weekly emails, they could receive both emails. You can adjust communication limits in your admin section and also within each smart campaign -- although be careful with something like a webinar, you wouldn't want someone who had registered for a webinar to miss a follow up email because you limited communications.
We're using them for nurture right now, on a pretty basic level. Mostly to re-engage, and accelerate people through and into our sales cycle. Just this week I tried to set up an onboarding campaign, but found that we had too much crazy logic going on, so I eventually went back to standard programs and smart campaigns. I see value in both types of programs.... but for standard nurturing, engagement programs are great!
Hope this helps, let me know if you have additional questions!