The dates for our 07/2025 charter are about to open up and I have a question about ticketing when using FF miles for one leg and paying for the second leg.

Our miles are on Delta. We're coming from Houston but looking at the ATL to either SJU or STT part, flying to SJU gives us a lot more flexibility. I know (assume?) we can't use miles for the code share SJU - EIS part but for traveling simplicity, like possibly not having to recheck bags in SJU, wondered if Delta would ticket the entire itinerary.

I would highly doubt that airline will ticket beyond flight you purchased with them. If code share, yes.

I just went through something kind of similar with Delta on our next flight into STT. Everyone in the family had enough miles to get one leg free. So I called Delta and asked what to do. They said I had to book everything separately. So I had to get separate tickets for all 4 of us by using everyone's own skymiles account. Luckily I was still able to pick all our seats next to each other. Then the return I had to book a separate trip.
I know it's not your exact situation but I think the takeaway is that you'll have to book your legs separate.

The SJU to EIS would be on a Delta code share which currently seems to be mostly Cape Air with a Silver flight in the mix. My exact dates aren't open yet so I can't be sure about that.

Normally you can use miles on a code share flight. You might want to call Delta directly and see if it can be booked.
G

Thanks George. I'll give them a call when the dates open up.